[gmx-users] g_order post - 3.3.1 (yes, again).
Hello all, I've been having a nightmare of a time trying to get order parameters for my lipids. All pre-3.3 files I have can be processed quite happily with a version of g_order from 3.2.1, but I can't seem to get 4.0 (or 3.3.1) to produce the basic order.xvg. I've tried specifying all carbons to be calculated in a single group - order.xvg never gets produced. Specifying each equivalent atom in a different group, as worked for 3.2.1, doesn't work either - it only asks for one group, and even if you specify one group to just give it one type of carbon, that still doesn't produce order.xvg. I get sg-ang and sk-dist (although sg-ang is a long sequence of zeroes at each timepoint), so the program is working, just not giving out the result I want at the end. Does anyone have an idea what I'm doing wrong, or alternatively have a protocol that they know works for them? Technical stuff for the approach I use that I think SHOULD work (have tried several other variations): Commands I run (leaflet.ndx contains atoms from one leaflet in group 0, other leaflet in group 1): make_ndx -f $tpr -n leaflet -o testyleaf2 <<+ t LP2 | t LP3 | t LC | a C24 | a C25 | a C45 | a C46 1 & 2 del 0 del 0 del 0 q + /home/ad0303/GROMACS4/bin/g_order -s $tpr -f trjShort -o test -n testyleaf2 -nice 0 -szonly result: Reading file topol1.tpr, VERSION 3.2.1 (single precision) Reading file topol1.tpr, VERSION 3.2.1 (single precision) Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: Group 0 (leaflet2_&_LP2_LP3_LC_C24_C25_C45_C46) has 2304 elements There is one group in the index Reading frame 0 time 0.000 Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.3# Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.3# Reading frame 60 time 45.750 gcq#151: "I Ripped the Cord Right Out Of the Phone" (Capt. Beefheart) files output: sg-ang.xvg, sk-dist.xvg sg-ang.xvg (small excerpt): 0.00 0.00 0.75 0.00 1.50 0.00 2.25 0.00 3.00 0.00 3.75 0.00 4.50 0.00 5.25 0.00 6.75 0.00 7.50 0.00 sk-dist.xvg 0.00 0.025605 0.75 0.025660 1.50 0.025662 2.25 0.025649 3.00 0.02 3.75 0.025473 4.50 0.025505 5.25 0.025541 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulation of mixed enantiomers
The topologies should not be identical, surely? Check out the section on improper dihedrals in the manual, it's possible to specify an improper to keep enantiomers in their intended handedness. - Original Message From: Anthony Costa <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Friday, October 10, 2008 8:45:55 PM Subject: [gmx-users] simulation of mixed enantiomers i have a simulation where i would like to study the interaction of N small molecules of various enantiomeric composition. if i use a simple R+S situation (N=2) by inserting the other enantiomer into my already created box, subsequent minimization either yields unphysical structures for the inserted enantiomer or will often reverse its symmetry to that of the original molecule. i am clearly missing something about the configuration of a reasonable topology for this type of system, but i'm can't quite figure it out. not surprisingly, i get errors when creating the mdp file for my energy minimization. the topologies created for both R and S enantiomers are identical, as i would expect (in this case they are small amino acid residues), when created individually, so i usually just increment the number of molecules in my original topology file after inserting the opposite enantiomer. WARNING 1 [file "topol.top", line 159]: 13 non-matching atom names atom names from topol.top will be used atom names from 2_2mer.gro will be ignored what am i missing? thanks for your time, anthony -- Anthony B. Costa Purdue University Department of Chemistry 560 Oval Drive, #365 West Lafayette, IN 47907 ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] increasing membrane bilayer size
Please search the message archives for the thread entitled "Leaflet of Bilayer" that discussed this precise task just a couple of weeks ago. - Original Message From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: "gmx-users@gromacs.org" Sent: Saturday, October 4, 2008 11:00:22 PM Subject: [gmx-users] increasing membrane bilayer size Hi, I have a popc bilayer (126 lipids) and would like to increase its size (in both x and y direction) so that it contains 288 lipids. How can I do this ? Many thanks Shozeb ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Leaflet of Bilayer
(Yes, what Chris Neale said). I had to do something similar myself, to make a 256-lipid square box from a 128 lipid box. I used genbox to make a new, larger square box using my original lipid patch as the input file, and then tinkered with the dimensions to get the lipids/leaflet as close to what I wanted as possible, then deleted the excess 1 or 2 lipids in one leaflet. I wrote a small script to count the lipids in each leaflet, it's not hard to code and I found it immensely useful for generating leaflet-specific index files later. I must admit, I only actually equilibrated it for 20ns or so. - Original Message From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, September 22, 2008 6:55:37 AM Subject: [gmx-users] Leaflet of Bilayer In my opinion, use any technique that you want (genbox included) then run the resulting system for >=50ns while plotting the area per lipid and order parameters over time. When these values stop drifting over time then you have an equilibrated bilayer. If you have access to a cluster that scales well to 4 cores then this should not take longer than a month. With systems that scale well to 10 cores I can equilibrate such a system in under two weeks. Of course, the more limited your resources are then the more thought that you need to put into your setup. Very generally, for beginners with at least moderate computational resources, I suggest immediately following your first good idea to get the system prepared and then, while it is running, starting to think about how it could have been done in a better way. With cpu resources as they are now, your initial run is likely to be finished faster than anything else if you start it immediately and the next time you go about this it will be faster because you will figure out the better method. Bottom line: an equilibrated bilayer is an equilibrated bilayer, and I as a reader am not going to have any problem with your final results even if I think that you could have obtained an equilibrated bilayer with a quicker method. Important note: Please use a new subject for a new topic. I know that topics often diverge, but you started this thread with a vmd-list question and now you are on to something that is only related to that by the fact that you study membranes. Chris. --- original message --- Thanks for the response Just diverting this topic to about specific number of popc molecules. I created the bilayer by using genconf command genconf -f popc128a.pdb -o out.gro -dist 0 0 0 -nbox 2 1 1 (as I posted in my previous mail) generated output file contain 128 popc in each leaflet of bilayer. If you see original popc box dimensions 6.1x6.2x6.9 (means in all dimensions popc number almost same)but with genconf command above mentioned options created box values 12x6.1x6.9. I dont want that many popc molecules because in X-dimension too many popc molecules are present. 1.is there anyway to reduce those popc molecules from 128 to 80/90 popc molecules? or 2.I wanted to create popc molecules 80 or 90 in eachleaflet is it possible to generate? These are may be trivial queries Could you give suggest me please Thanks in advance. ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] make_ndx "one of your groups is not ascending"
I'm having trouble with using make_ndx with a specific file. Whenever I try to combine or use a specific group (group content at bottom) I get the error "One of your groups is not ascending", and the group is not actually included in the subsequent group produced. As far as I can see, the numbers in the group are in ascending order (as it ought to be, the group was generated by make_ndx in a previous step). So can anyone explain what the error is trying to tell me? The process has been used many times with other simulations, it's just this one that seems to be rickety. [ LP3_&_leaflet1 ] 503 524 557 578 665 686 720 739 2657 2678 2765 2786 2819 2840 3035 3056 3143 3164 3197 3218 3251 3272 3412 3431 5281 5302 5443 5464 5497 5518 5551 5572 5767 5788 5875 5896 6036 6055 6089 6108 7905 7926 7959 7980 8229 8250 8283 8304 8520 8660 8679 10529 10550 10583 10604 10691 10712 10799 10820 10907 10928 11144 11178 11197 11231 11250 11337 11356 13153 13174 13315 13336 13369 13390 13477 13498 13531 13552 13768 13802 13821 13855 13874 15777 15798 15885 15906 15939 15960 16155 16176 16209 16230 16263 16284 16392 16426 16445 16479 16498 16532 16551 16585 16604 18506 18527 18560 18581 18668 18689 18776 18797 18884 19013 19047 19066 19153 19172 21019 21040 21127 21148 21181 21202 21235 21256 21343 21364 21397 21634 21668 21687 21774 21793 23640 23661 23694 23715 23802 23823 23856 23877 23964 23985 24018 24039 24180 24201 24255 24395 24414 26261 26282 26315 26336 26369 26390 26423 26444 26477 26498 26639 26660 26876 26963 26982 27069 27088 28882 28903 28936 28957 29044 29065 29152 29173 29206 29227 29497 29531 29550 29637 29656 31611 31632 31665 31686 31719 31740 31827 31848 32118 32205 32224 32258 32277 34178 34199 34286 34307 34448 34739 34739 34826 34845 34932 34951 36799 36820 37123 37360 37394 37413 37447 37466 37500 37519 37553 37572 39474 39495 39528 39549 39582 39981 40068 40087 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Corrupt TRR file -- skipping a bad frame?
I'm sure I have, in the past, found a way to use trjcat/trjconv to overwrite a bad frame with a good one. From memory, I had to convert the area around the bad frame to pdb/gro (for some reason that worked where normal tools didn't), open up the files, rewrite several bad frames (just copied and pasted good frames onto it), and then converted it back to trr/xtc. It may have only worked due to being a special case, but it might be worth looking for that in the archives - I remember mentioning it before. I'd love to know what the rules are for which file trjcat takes frames from, when there's an option, actually... - Original Message From: Tsjerk Wassenaar <[EMAIL PROTECTED]> To: [EMAIL PROTECTED]; Discussion list for GROMACS users Sent: Wednesday, August 27, 2008 9:21:10 AM Subject: Re: [gmx-users] Corrupt TRR file -- skipping a bad frame? Hi Matt, You can determine the size of a single frame in bytes from what you have and use 'split' to split up your corrupt trajectory. Now the corrupt frame may not have the correct size, so you'll probably have to think of a way to start splitting from the end. Cheers, Tsjerk On Wed, Aug 27, 2008 at 1:10 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > Matt Wyczalkowski wrote: >> >> I have a corrupt TRR file with a bad frame in the middle; I am >> wondering if I can remove just the bad frame to utilize all of my good >> data. >> >> To obtain the corrupt TRR file, I first ran a simulation which died >> (at about 37.9ns) due to a disk quota restriction; this first >> simulation produced part1.trr. I restarted this simulation, and >> obtained part2.trr after the simulation finished successfully. I then >> used trjcat to concatenate these simulations (not aware that part1.trr >> ended on a corrupt frame), and the data were appended to part1.trr. >> Finally, to save disk space, I deleted part2.trr, confident that all >> 60ns of simulation data were in part1.trr. > > Lesson learned in being careful :) > >> >> Not surprisingly, when I run any sort of analysis tool (including >> gmxcheck) it quits when it gets to the corrupt frame. Ideally, I >> would like to remove just the offending frame. I can use trjconv to >> extract the data up to the bad frame, but I can't use that utility to >> extract the good data past the bad frame, since it dies at the bad >> frame. > > Unfortunately, even to extract frames, that bad frame has to be read, which > will cause everything to crash. > > The best bet is just to do it again. Extract the viable data from the first > part of the simulation and pick up from that point. Then concatenate, check > your output :), and proceed. > > -Justin > >> >> For what its worth, part1.trr from the original run was about 2.1Gb, >> and part1 + part2 are about 3.4Gb. >> >> Any ideas how I could recover good data in a TRR file past a bad frame? >> >> Regards, >> >> Matt Wyczalkowski >> ___ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.or
Re: [gmx-users] Order parameters of lipid
Yes, I never managed to get a later version of g_order to function properly. I only ever get the -Sg and -Sk outputs, no matter WHAT I put in the index files. I've just kept an old version of gromacs on the machine I use for analysis. A copy of 3.2.1 should be quite easy to download, and will definitely work using the approach you've been told. I'm pretty sure that if you get it wrong, you just end up with empty output, so if you get numbers then you're doing it right. Incidentally, I always get a sawtooth-shaped curve from my g_order. Anyone know if this is something simple, like a sampling issue, or indicative of something more serious? I'm fairly sure I've seen it in published MD work with bilayers, but that doesn't mean it's right of course. - Original Message From: Justin A. Lemkul <[EMAIL PROTECTED]> To: Gromacs Users' List Sent: Friday, August 1, 2008 11:19:33 AM Subject: Re: [gmx-users] Order parameters of lipid minnale wrote: > > > Thanks to Justin for his suggestion > I tried the way mentioned in http://wiki.gromacs.org/index.php/make_ndx. > I made index file with seperate groups and feed to g_order command > g_order -f .xtc -s .tpr -od scd.xvg -o ord -n .ndx > Group 0 ( C34) has 128 elements > Group 1 ( C36) has 128 elements > Group 2 ( C37) has 128 elements > . > . > . > . > . > . > . and so on till Group 15 ( C50) has 128 elements > > here I am bit confused which group to select , and i selected 1 group? > Is it correct?? > Any make me clear about this problem > Thanks in advance. > > Which version of Gromacs are you using? I recall some weird behavior from version 3.3.1(?) that I could never get around. Version 3.3, for example, automatically recognizes all the groups in the index file and calculates the order parameters along the chain. I don't know if 3.3.1(?) allows you to select multiple groups, but that's what you'd be after - all the groups in the index should be part of the analysis. -Justin > > On Thu, 31 Jul 2008 Justin A.Lemkul wrote : > >Read about how to create the appropriate index file here: > > > >http://wiki.gromacs.org/index.php/make_ndx > > > >There are also several posts in the list archive on how to create the > index file correctly. > > > >-Justin > > > >minnale wrote: > >> Thanks Justin for your prompt reply with better suggestion > >>I have done like this > >>1.For index file > >> Selected > a C34 > >> 3 34 :128 elements > >> then > >> > a C36 > >> 4 36 : 128 elements.. > >> till C50( only C atoms) > >>so > >>index file contain > >> [C34] > >> atoms > >> [36] > >> atoms...[C50] > >> > >>2. then I have typed command like this > >> g_order -f .xtc -s .tpr -o ord.xvg -od scd.xvg -n .ndx > >> asked to select group > >>Group 0 ( System) has 14036 elements > >>Group 1 ( POPC) has 6656 elements > >>Group 2 ( SOL) has 7380 elements > >>Group 3 ( C34) has 128 elements > >>Group 4 ( C36) has 128 elements > >>. > >>. > >>. > >>Group 18 ( C50) has 128 elements > >> > >>Group Select a group: 3 > >>Selected 3: 'C34' > >>Reading frame 0 time 0.000 Back Off! I just backed up > sg-ang.xvg to ./#sg-ang.xvg.1# > >> > >>Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1# > >>Last frame 25000 time 5000.000 > >>gcq#189: "Stay Tuned, We'll Be Right Back" (CNN) > >>have I done is correct? > >> > >>I have doubt that the mentioned -o and -od flags didnt generate .xvg > file but without mentioning -Sk and -Sg flags .xvg got generated? > >>Can you clear this problem. > >>Thanks in advance. On Thu, 31 Jul 2008 Justin > A.Lemkul wrote : > >> > > >> > > >> >minnale wrote: > >> >> I want to calculate order parameters of palmitoyl and oleyl > chains of POPC which ran it for 5ns, so I have done below mentioned steps. > >> >>1. First I tried for Palmitoyl, so I made .ndx file by using > make_ndx command and selected a C34|a 035|a C36.a C50. > >> >>In index file the palmitoyl chain selected like this > C34_O35_C36..C50 > >> >> > >> > > >> >You need the index groups to specify each atom separately, and > only include carbon atoms. Your index group will be something like: > >> > > >> >[ C34 ] > >> >(atoms) > >> >[ C36 ] > >> >(atoms) > >> >etc. > >> >[ C50 ] > >> > > >> >>2. This index file feed to g_order command > >> >> g_order -f .xtc -s .tpr -n palmit_ord.ndx -o order -od > scd.xvg -unsat > >> > > >> >There are no unsaturated carbons in a palmitoyl chain. > >> > > >> >-Justin > >> > > >> >> This programming is running very slowly > >> >>Have I done any mistake here? > >> >>I would be thankful for your help > >> >> >> > >> >> > >> >> > >> > >> > >> >> > >> >>___ >
Re: [gmx-users] how to edit pdb file
Copy file, editconf to translate, then concatenate that with the original, reorder and renumber everything; or genbox will also do something similar with less tinkering. - Original Message From: "Wei, Xiupeng" <[EMAIL PROTECTED]> To: "gmx-users@gromacs.org" Sent: Wednesday, May 21, 2008 3:24:46 PM Subject: [gmx-users] how to edit pdb file Dear GMX users, I have a basic question. I want to put two same box in x direction. So I need increase the number of atoms and change their x coordinates,then combine it with the original one. But the file created by Excel can't be recoganized by gromacs. Is there any method in Gromacs to handle that? I also used Matlab, but it can't read pdb file correctly. Thanks. Best regards, xiupeng ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Re: water distortion above bilayer
How about you try the different options, see what they do, and then decide for yourself how best to utilise them for whatever it is that you wish to do? - Original Message From: ANINDITA GAYEN <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, May 19, 2008 2:28:30 PM Subject: [gmx-users] Re: Re: water distortion above bilayer How to be sure that the water is moving from the leaflet to the other leaflet? Can I see it from any analysis? How can i trace a water that is moving due to pbc and how to originate a pdb that will show the pdb that will be visually good for analysis (I am confused about the -pbc nojump and -pbc whole comands). Please send suggestions. Message: 5 Date: Mon, 19 May 2008 16:14:52 +1000 From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] water distortion above bilayer To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=UTF-8; format=flowed ANINDITA GAYEN wrote: > Hi all, > > In the TIP4P water layer above my dmpc bilayer after 100ps (OPLS-BERGER) > a hole is being formed. Some water molecules are absent in the water > layer, but the total no of water molecules are same. This is my semi.mdp > file This sounds like normal behaviour under periodic boundary conditions. Check the other side of the boundaries. See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Mark Unlimited freedom, unlimited storage. Get it now ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cutting the trajectory in small subtrajectories
Yes, that's exactly what the first reply was telling you. The option is "stride", I believe. - Original Message From: serdar durdagi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, May 13, 2008 8:44:37 AM Subject: Re: [gmx-users] cutting the trajectory in small subtrajectories Dear Florian, I want to analyze, trajectory files. So, I need all frames. by the way, in VMD is there any option to use every 10th or 20th frame? Thanks Serdar Florian Dommert <[EMAIL PROTECTED]> schrieb: serdar durdagi wrote: > Dear all, > > I made a simulation with 2.5 ns (with 12500 frames), when I want to > open this *.xtc file in VMD, it fails. it can read around 50% of > frames and than complains low virtual memory (actually I am using a PC > that has 1GB RAM). Hello, if you just want to watch the movie using vmd, don't use every frame, when opening the xtc-file. Perhaps every 10th or 20th is enough and you won't get out of memory. Best Regards Flo > > Thus, I would like to cut my *.xtc file to small subtrajectory files. > In gromacs manual, it says it is possible with trjconv option together > with sub. But it's not clear how can I give a command let's say to > divide my whole trajectory file to 5 subtrajectories. > > Thank you very much in advance for your comments. > > > Serdar > > > > > > Nicht vergessen! Am Sonntag, den 11. Mai ist *Muttertag > * > Geschenkideen, Gedichte & mehr: www.yahoo.de/muttertag > . > > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Computational and Theoretical Softmatter & Biophysics group Frankfurt Institute for Advanced Studies Johann-Wolfgang-Goethe University Ruth-Moufang-Str. 1 60438 Frankfurt am Main Phone: +49(0)69 / 798 - 47522 Fax: +49(0)69 / 798 - 47611 EMail: [EMAIL PROTECTED] Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Nicht vergessen! Am Sonntag, den 11. Mai ist Muttertag Geschenkideen, Gedichte & mehr: www.yahoo.de/muttertag. Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Unable to neutralize my system
You haven't edited your topology files correctly. If changing the number of ions has not resulting in a change of charge, I'd suggest you haven't added the ions in right; otherwise, I suspect it's something to do with the number of waters. Particularly as the error in coordinates vs. topology is divisible by 3. - Original Message From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Thursday, May 8, 2008 11:34:20 AM Subject: [gmx-users] Unable to neutralize my system Dear All When I run the command "genion" specifying the number n type of chrges to be added, it works fine. I also have made changes in my topology file. But somwhow when I run the "grompp" after that it gives me the following error... processing topology... Generated 380 of the 1326 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 2 bonded neighbours for SOL 2818600 Excluding 1 bonded neighbours for Na+ 2 NOTE: System has non-zero total charge: -2.39e+01 processing coordinates... --- Program grompp_mpi, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (ce_myoII_frag0_neu.gro, 8461523) does not match topology (ce_myoII_frag0.top, 8461535) --- I tried adding 2 and 3 ions to the system. But it seems to give the same error. Could someone help? Thanks Namitha Mohandas ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with g_order
I suggest you search the archives too. This has been discussed several times. - Original Message From: pragya chohan <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, April 30, 2008 9:52:19 AM Subject: [gmx-users] problem with g_order Dear users I am calculating order parameters of palmitoyl which has 16 carbons. I made the index file with all 16 atoms selected . but the output file has only 14 atoms listed. I have cross-checked the index file. what can be the problem? I am using 3.3 version Thanking you Pragya Chohan Windows Live Spaces : Help your online world come to life, add 500 photos a month. Try it! Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to center my trimer in my simulation box.
I've often found it necessary to do multiple trjconv steps to get the result I want. So in this case, I'd probably make sure my protein is genuinely centered in the box, then take that output .xtc and then make sure everything is whole and approximately in the box (-pbc whole). - Original Message From: Ilya Chorny <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, April 22, 2008 11:52:23 PM Subject: Re: [gmx-users] How to center my trimer in my simulation box. So I got it to center my protein (using -pbc nojump) and keep the trimer and the membrane in tact but it completely destroyed my water. I was hoping I could get the whole simulation box back with the protein in the center. Is that possible? Thanks, Ilya On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny <[EMAIL PROTECTED]> wrote: Just to clarify. I would run trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro? What would I run next? Thanks, Ilya On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <[EMAIL PROTECTED]> wrote: On Tue, 22 Apr 2008 14:14:19 -0700 "Ilya Chorny" <[EMAIL PROTECTED]> wrote: Hello, I am simulating a trimer in a membrane. In one of my simulation two of the monomers are on one side of the box and the other monomer is on the other side of the box. I tried using trjconv to center the whole thing in the center of my simulation cell but have failed miserably. I also searched around for about an hour and could not find anything. I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro. first run trjconv -pbc nojump Any advice? Thanks, Ilya -- Ilya Chorny Ph.D. - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D. Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes 2 monolayers (shift in box center?)
It sounds like you have it pretty clear already. A point to note, in GROMACS the origin coordinate 0,0,0 is at a corner of the box, not the centre. This could be what caused such a big (apparent) shift. - Original Message From: maria goranovic <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, March 31, 2008 10:32:28 AM Subject: [gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes 2 monolayers (shift in box center?) Hello Folks, I am simulations a lipid bilayer. After minimization, the output .gro file contains a bilayer that is a layer of water sandwiched between 2 monolayers of lipids (instead of being the other way around). I guess this has something to do with the periodic shift in boxes or something. Can someone please clarify this for me ? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen Special deal for Yahoo! users & friends - No Cost. Get a month of Blockbuster Total Access now http://tc.deals.yahoo.com/tc/blockbuster/text3.com___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours
The end of the log files after the simulation finishes might help you understand if there's anything odd that's taking more computation than normal. Also, just one extra running process can slow down the entire simulation as all processors will wait for the slowest. Check if it takes as long if you run it again. - Original Message From: Carsten Kutzner <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, March 24, 2008 1:19:34 PM Subject: Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours Am 24.03.2008 um 10:17 schrieb maria goranovic: > Hi Folks, > > My simulation is running too slow. It took 10 wall clock hours (40 > cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC > bilayer. The hardware is a 4-cpu core. The installation is gromacs > 3.3.1. I have run much larger systems (~ 16 atoms) using the > same gromacs installation on the same hardware, and they run much > faster than this (200 ps per 40 cpu hours). > > Can anybody suggest why this is happening ? Is it because of latency > in the cpu communication? If so, what is the workaround ? Is there a special reason for using pme_order=5? I would use the default, 4 instead, or at least an even number. Carsten > My .mdp script is below. > These are the run commands. > > grompp -np 4 -v -f heat.mdp -c minim4.gro -p dppc.top -n dppc.ndx -o > heat.tpr > mpirun -np 4 ~/bin/mdrun_mpi -np 4 -v -s heat.tpr -o heat.trr -c > heat.gro -e heat -g heat.log > & heat.out > > ;### > ; heat.mdp > ; > title = heating > cpp= /usr/bin/cpp > constraints= hbonds > constraint_algorithm = lincs > unconstrained_start = yes > integrator = md > nsteps = 25000 > dt = 0.002 > comm_mode = linear > nstxout= 5000 > nstvout= 5000 > nstlog = 5000 > nstenergy = 5000 > nstlist= 10 > ns_type= grid > pbc= xyz > ; -- > coulombtype= PME > rcoulomb= 1.0 > vdwtype= cut-off > rlist = 1.0 > rvdw= 1.0 > fourierspacing = 0.1 > pme_order = 5 > ewald_rtol = 1e-5 > ; --- > ; Berendsen temperature and preasure coupling > Tcoupl = berendsen > tc-grps= DPPC SOL > tau_t = 0.6 0.6 > ; i have also tried a tau value of 0.1, but no speed up > ref_t = 323.0323.0 > Pcoupl = berendsen > Pcoupltype = semiisotropic > tau_p = 1.01.0 > compressibility= 4.5e-5 4.5e-5 > ref_p = 1.01.0 > ; --- > gen_vel= yes > gen_temp= 323.0 > gen_seed= 194040 > ;### > > -- > Maria G. > Technical University of Denmark > Copenhagen ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tutorial for membrane-bound systems
I recommend the GROMACS manual. Particularly chapter 5. Oh, and the wiki - http://wiki.gromacs.org/index.php/Category:Tutorials - Original Message From: serdar durdagi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, March 20, 2008 8:52:15 AM Subject: Re: [gmx-users] tutorial for membrane-bound systems Dear Alan, You are right a DPPC unit has less than 300 atoms, but I have 189 units. How can I apply PRODRG for 189 different coordinate files to convert to necessary GROMACS coordinate file? It must be very tedious. I am using ligand-enzyme tutorial for Gromacs. But for membrane-bound case I guess this tutorial is not enough to work. Best Wishes, Serdar Alan Dodd <[EMAIL PROTECTED]> schrieb: Firstly, a molecule of DPPC has less than 300 atoms. Secondly, I'd suggest you look for stuff by Tieleman, White, or Sansom. Googling/literature searching any of these names with "membrane" should give you some rough pointers on how it's been done in the past. There is no official membrane tutorial, however. There is a ligand/receptor one out there somewhere I think? - Original Message From: serdar durdagi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, March 20, 2008 2:00:49 AM Subject: [gmx-users] tutorial for membrane-bound systems Dear all, I would like to make MD simulations of a drug at the binding site of the receptor sorrounded by DPPC. pdb coordinate file of all DPPC units (189 units, 1 unit has 130 atoms) are described seperately. I was using Dundee PRODRG server for generating .itp and drgpoh2.pdb files for the drug. Since this program is limited to convert files up to 300 atoms, I couldn't use it for the DPPC units for constructing a full drgpoh2.pdb file for the DPPC. Is there any tutorial of GROMACS for this kinds of systems? Kind Regards, Serdar Durdagi Lesen Sie Ihre E-Mails jetzt einfach von unterwegs.. -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your homepage.___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php E-Mails jetzt auf Ihrem Handy.. -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tutorial for membrane-bound systems
Firstly, a molecule of DPPC has less than 300 atoms. Secondly, I'd suggest you look for stuff by Tieleman, White, or Sansom. Googling/literature searching any of these names with "membrane" should give you some rough pointers on how it's been done in the past. There is no official membrane tutorial, however. There is a ligand/receptor one out there somewhere I think? - Original Message From: serdar durdagi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, March 20, 2008 2:00:49 AM Subject: [gmx-users] tutorial for membrane-bound systems Dear all, I would like to make MD simulations of a drug at the binding site of the receptor sorrounded by DPPC. pdb coordinate file of all DPPC units (189 units, 1 unit has 130 atoms) are described seperately. I was using Dundee PRODRG server for generating .itp and drgpoh2.pdb files for the drug. Since this program is limited to convert files up to 300 atoms, I couldn't use it for the DPPC units for constructing a full drgpoh2.pdb file for the DPPC. Is there any tutorial of GROMACS for this kinds of systems? Kind Regards, Serdar Durdagi Lesen Sie Ihre E-Mails jetzt einfach von unterwegs.. -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to change the default value for pbc ?
Editing mdout.mdp will not affect the parameters in your .tpr, and therefore
your simulation, I'm fairly sure. It's just a report of what you've specified,
with all the defaults.
Add the pbc=whatever line into your INPUT mdp to fix this.
- Original Message
From: Liu Shiyong <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Thursday, March 13, 2008 11:39:46 PM
Subject: [gmx-users] How to change the default value for pbc ?
Hi,
I generated mdout.mdp
by grompp -f em.mdp -c ${file}_box.gro -p ${file}.top -o ${file}.input.tpr .
The pbc in mdout.mdp is like:
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
It seems that grompp doesnot give an option to change the pbc value.
I didnot find an easy way to change the pbc value . The only way I found is to
edit the mdout.mdp directly.
Best
--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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Re: [gmx-users] trjconv output at a specified time
Select a group: 2 Selected 2: 'Protein-H' trn version: GMX_trn_file (single precision) Reading frame 0 time 125.000 'nuff said. Couldn't comment on the time between frames in your file. gmxdump will tell you, or get it from (nstxout or nstxtcout)*dt in your mdp. - Original Message From: Liu Shiyong <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Wednesday, March 12, 2008 11:24:00 PM Subject: Re: [gmx-users] trjconv output at a specified time Thanks. The trajectory starts at 125ps ? So step 1 == 125 ps step 2 == 250 ps step 3 == 375 ps Where is 125ps from ? But ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.002 On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: You asked for the frame at 1ps. The trajectory starts at 125ps, so unsurprisingly the program does not give you an output. - Original Message From: Liu Shiyong <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Wednesday, March 12, 2008 10:07:17 PM Subject: [gmx-users] trjconv output at a specified time Hi, I want to output a structure in a given time, for example , in step 1 during minimization. I tried the following command using dump: trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s r-l_1_oplsaa.input.tpr -t0 0 -dump 1 But It didnot work. Output msg: Select a group: 2 Selected 2: 'Protein-H' trn version: GMX_trn_file (single precision) Reading frame 0 time 125.000 Back Off! I just backed up m.pdb to ./#m.pdb.1# Last frame 19 time 2418.000 WARNING no output, trajectory ended at 2418 gcq#76: "Baseball Heroes Only" (P.J. Harvey) Best -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv output at a specified time
You asked for the frame at 1ps. The trajectory starts at 125ps, so unsurprisingly the program does not give you an output. - Original Message From: Liu Shiyong <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Wednesday, March 12, 2008 10:07:17 PM Subject: [gmx-users] trjconv output at a specified time Hi, I want to output a structure in a given time, for example , in step 1 during minimization. I tried the following command using dump: trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s r-l_1_oplsaa.input.tpr -t0 0 -dump 1 But It didnot work. Output msg: Select a group: 2 Selected 2: 'Protein-H' trn version: GMX_trn_file (single precision) Reading frame 0 time 125.000 Back Off! I just backed up m.pdb to ./#m.pdb.1# Last frame 19 time 2418.000 WARNING no output, trajectory ended at 2418 gcq#76: "Baseball Heroes Only" (P.J. Harvey) Best -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Relating acceleration to pressure
f=ma? - Original Message From: avinash kumar <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, March 4, 2008 7:08:04 PM Subject: [gmx-users] Relating acceleration to pressure Hello all, This is more of a theoretical question than relating to the software. My question is that when we simulate a pressure driven system (that is I am trying to simulate a nanochannel fluid flow using GROMACS) the pressure is being implemented by defining the group of fluid atoms as one acceleration group and giving required acceleration. How can we correlate a actual pressure and accleleration of one individual particle . That is what is the statistical formula which will give the relation. Thanks in advance, Avinash ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to ask pdb2gmx to print all parameters in the itp file
If you convert the tpr binary into a text file, it should have every parameter in it I think? - Original Message From: LeeHui <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Friday, February 15, 2008 4:57:13 PM Subject: [gmx-users] How to ask pdb2gmx to print all parameters in the itp file Dear all gmx users, I am converting the parameters in "itp" file into DL_POLY format, and will be using it in my own version of DL-poly. I was wondering if there is a way to ask pdb2gmx or some other utilities in Gromacs to print all the parameters into itp, so I don't have go to the database and find them out. eg. the default pdb2gmx generated itp have this format [ angles ] ; aiajak functc0c1c2c3 1231 1241 1251 3241 instead of leaving c0, c1.. blank, I want the exact values of them printed . Is there a way to this in Gromacs ? Thanks, Hui _ Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！ http://get.live.cn/product/photo.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dist producing inconsistent values
- Original Message From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, February 7, 2008 6:35:55 PM Subject: Re: [gmx-users] g_dist producing inconsistent values [EMAIL PROTECTED] wrote: >> I've since found the source of my problem - the program was measuring >> the (marginally shorter) distance across the PBC boundary, rather than >> the distance >> within the box. Unfortunately there doesn't seem to be a way to turn >> PBC images off (correct me if I'm wrong?), so I guess I'm going to do >> some jiggerypokery with the data and some math. > Distance larger than half a box size are ill-defined anyway in a PBC simulation. -What do you mean? I'd assumed that simply having enough water separating a bilayer from its periodic image that no water 'saw' both bilayers would be sufficient; is this not the case? In some special cases you can do this, for instance within a protein it would work. I've implemented -nopbc options in some programs but not in g_dist yet. Please put it on the developer wishlist. on the wiki. -Done. Until then, I'm using g_traj -ox -com and doing the math with my own script. Many thanks for the various alternative techniques suggested. Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dist producing inconsistent values
I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to do some jiggerypokery with the data and some math. - Original Message > I've been using g_dist to plot distances along the normal to my bilayer > between groups. Namely in this case, between the phosphates of opposing > leaflets, and the peptide. I would expect the sum of the distances > between the peptide and each leaflet's phosphates to equal the distance > between the two sets of phosphates. But they mysteriously don't. I'm > taking the z-distance to be the final value in each row, as the headers > in the .xvg indicate: > > @ s0 legend "|d|" > @ s1 legend "d\sx\N" > @ s2 legend "d\sy\N" > @ s3 legend "d\sz\N" >0.0003.28371450.0671294 -0.0351439 -3.2828403 > > The index groups are definitely correct (doublechecked by using trjconv > -n -dump and visualising the groups so selected), so there's no error > there, I'm sure. And these are the numbers I get out for the first frame: > Peptide - leaflet 1 phosphates:-3.3361144 > Peptide - leaflet 2 phosphates:0.2953452 > Leaflet 1 - leaflet 2 phosphates:-3.2828403 > Is there an error in my understanding of how this is working? I'm pretty > certain the first two numbers should sum to the value of the third > number. Alternatively, any idea what could be going wrong? The files > being used are definitely the same, too... > > Alan. > > > > _ > ___ Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dist producing inconsistent values
I've been using g_dist to plot distances along the normal to my bilayer between groups. Namely in this case, between the phosphates of opposing leaflets, and the peptide. I would expect the sum of the distances between the peptide and each leaflet's phosphates to equal the distance between the two sets of phosphates. But they mysteriously don't. I'm taking the z-distance to be the final value in each row, as the headers in the .xvg indicate: @ s0 legend "|d|" @ s1 legend "d\sx\N" @ s2 legend "d\sy\N" @ s3 legend "d\sz\N" 0.0003.28371450.0671294 -0.0351439 -3.2828403 The index groups are definitely correct (doublechecked by using trjconv -n -dump and visualising the groups so selected), so there's no error there, I'm sure. And these are the numbers I get out for the first frame: Peptide - leaflet 1 phosphates:-3.3361144 Peptide - leaflet 2 phosphates:0.2953452 Leaflet 1 - leaflet 2 phosphates:-3.2828403 Is there an error in my understanding of how this is working? I'm pretty certain the first two numbers should sum to the value of the third number. Alternatively, any idea what could be going wrong? The files being used are definitely the same, too... Alan. Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] analysis of POPC
You'd have thought the MD papers you have would also compare values against experimental data? These papers do exist, I'm sure, I came across the all the time while looking for DOPC data - though I didn't make a note of them. Plus the people who initially parameterised the POPC topology (Tieleman?) must have compared results to experimental data. In summary, try harder ;) - Original Message From: pragya chohan <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Saturday, February 2, 2008 12:54:35 PM Subject: RE: [gmx-users] analysis of POPC Thanks, but I did get some papers on the analysis done on POPC by MD but I did not get any experimental papers showing the values so that I can compare results of my MD with experimental data. If anyone happens to have such papers please send them to me at [EMAIL PROTECTED] > Date: Sat, 2 Feb 2008 07:20:54 -0500 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] analysis of POPC > > Quoting pragya chohan <[EMAIL PROTECTED]>: > > > > > hello users > > I am trying to do analysis after bilayer simulation. I cannot get any > > experimental data on POPC to validate my model with. Can the people who are > > working on same lipid tell me some references and also what analysis should > > be done of the bilayer before putting protein into it? > > I spent less than two minutes on Google and found papers giving all sorts of > experimental parameters (density, area per headgroup, bilayer thickness, > etc). > I suggest you try the same. > > In terms of the analysis you need to do, that is up to what question you are > asking and why you are simulating this particular lipid. Refer to the > literature and find papers by groups that have simulated proteins in POPC (and > perhaps proteins in membranes in general) to determine what they have found > relevant, and apply the same to your system. > > -Justin > > > _ > > Tried the new MSN Messenger? It’s cool! Download now. > > http://messenger.msn.com/Download/Default.aspx?mkt=en-in > > > > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Detailed profiles 4 marriage! Only at Shaadi.com Try it! -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Temperature without trr
Thankyou - a few hundred ps was quite doable. Temperature is (fortunately!) consistent between groups to well within a couple of degrees, which is probably fine, but I just want to check that the temperatures from groups in g_traj are directly comparable with each other? They're not the same as the ref_t which is consistent with g_energy, which is fine as I gather temperatures with g_traj are inherently out due to ignoring constraints; I'm assuming, though, that the different constraints from the molecules being different don't make the errors different... if you see what I mean? i.e. that the error due to not accounting for constraints is constant. Alan. - Original Message From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, January 29, 2008 9:45:01 PM Subject: Re: [gmx-users] Temperature without trr Alan Dodd wrote: > Gromacs users, > I want to look at the temperature difference between groups, to check whether > temperature coupling is working ok (specifically if the lipid is at the same > temperature as the water). > Unfortunately, I've rather foolishly deleted all my trrs due to a lack of > space, thinking xtc/edr would be all I needed. While I can get the *system* > temperature from g_energy, it doesn't take an index file, and g_traj needs > velocities (which I don't have any more). Anyone know of a way around this, > short of continuing the simulations and taking the .trr from that? > > Alan. If g_energy does only give you the system T it means you have not used T-coupling groups and hence your Temperatures will differ between lipid and water. Best way to know is to continue the simulation for few hundred ps and don't delete the trr :(. > > > > > Looking for last minute shopping deals? > Find them fast with Yahoo! Search. > http://tools.search.yahoo.com/newsearch/category.php?category=shopping > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Temperature without trr
Gromacs users, I want to look at the temperature difference between groups, to check whether temperature coupling is working ok (specifically if the lipid is at the same temperature as the water). Unfortunately, I've rather foolishly deleted all my trrs due to a lack of space, thinking xtc/edr would be all I needed. While I can get the *system* temperature from g_energy, it doesn't take an index file, and g_traj needs velocities (which I don't have any more). Anyone know of a way around this, short of continuing the simulations and taking the .trr from that? Alan. Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Checkpointing GROMACS jobs
If the runs all finish successfully, then incorporating run continuations into your script is simple, but I believe the issue may be more the tendency of tpbconv to fail unpredictably - should the .edr file be even one frame shorter than the .trr file due to a crash, for instance, then tpbconv will not be successful and your script dies. Parsing out the relevant error messages to produce the information required (for the option -time in this example) is presumably possible and would solve the problem, but it's not a trivial thing to script. Of course, the timescale of MD runs means that occasional manual intervention isn't too great a chore, but it can be annoying to almost complete a tpbconv on a very long run, only to find that it's missing the last couple of .edr frames due to a failure to flush the buffer... Alan. - Original Message From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, January 28, 2008 7:09:29 PM Subject: Re: [gmx-users] Checkpointing GROMACS jobs Steven Kirk wrote: > Hello, > > I have been using GROMACS for some very long (in wall clock terms) > simulations, and am curious as to how other users on this list solve the > problem of checkpointing long MD runs. It's a problem because of the > tendency of computational nodes in large HPC facilities (the more > processors, the more prevalent the problem, it seems) to keel over near > the end of a very time consuming run. Intermittent disk and scheduler > faults can also trigger such conditions. > > Checkpointing at the operating system level is very system-specific, and > occasionally compilers can produce executable 'dump' files that continue > from where your program left off, but I'm thinking that someone must > have automated this process directly using conventionally-compiled > GROMACS executables. > > Of course, it is possible to do an exact continuation from a crashed run > using .edr and trajectory (.trr) files by generating a new .tpr from the > last trajectory frame that had both position and velocity data. This > seems to be, by necessity, an entirely interactive process (unless > someone out there has a cool auto-restart script ..). > > I am thinking more in terms of 'proactive' checkpointing for long jobs, > by the following process: > > A script parses the desired .mdp file describing the user's MD run of T > timesteps, then asks the user how many sections (N) to split the run > into. The script will then auto-generate a shell script containing all > the necessary GROMACS commands to: > > * Generate a new .mdp file almost identical to the original, but with > the number of timesteps set to T/N. > > * Run N successive mdrun commands, where the output .trr and .edr files > from each short run using the modified .mdp file are used, to generate > an 'exact restart' .tpr file for the next 'mdrun' command, with the > appropriate continuation flag set. > > * Log (to a file) how many of the N partial runs have been completed, in > such a way that if the shell script containing the commands is > restarted, it will jump to the correct point in the sequence, restarting > from the most recently completed partial run. > > Has anyone else already solved this problem, or have a method > implementing some of the desirable properties above that I can then > extend to do exactly the things described above? > > Most queue system allow you to chain jobs, that is, let the next one start after the previous one finished. In PBS this is done alike qsub -Wdepend=afterok:prev_jobid combining this with a script to start the jobs you are all set. I presume you are aware of tpbconv -extend, or tpbconv -until ? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http
Re: [gmx-users] Specified frame doesn't exist or file not seekable
Check the bugzilla server, is it the same problem as #126? - Original Message From: Arnau Cordomi <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, January 21, 2008 2:12:17 PM Subject: [gmx-users] Specified frame doesn't exist or file not seekable Dear all, I'm getting the following fatal error every time I try to use trjconv or any analysis program with "-b" flag on my .xtr files: Program trjconv, VERSION 3.3.2 Source code file: trxio.c, line: 635 Fatal error: Specified frame doesn't exist or file not seekable I executed gmxcheck and all files seem ok. Without the "-b" flag everything works perfectly. Is this a bug? I found that the same issue was reported a few months ago for version 3.3.1: http://www.gromacs.org/pipermail/gmx-users/2007-November/030484.html Thanks in advance, Arnau ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] About g_msd (and noise)
I've been playing with g_msd myself recently, and been seeing weird results toward the end of the simulation. From the below post, it looks like I was doing it correctly (apart from analysing the leaflets separately). Previous posts in the mailing list have implied that increased noise towards the end of a simulation is inherent in the algorithm, I just wanted to check that I was interpreting those posts correctly? And if this is so, do people just not show the results towards the end? - Original Message From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Wednesday, January 16, 2008 6:48:32 AM Subject: Re: [gmx-users] About g_msd Justin A. Lemkul wrote: > Hi Alan, > > Thanks for the reply. My initial trajectory showed several of the lipids > jumped > across the box and continued through the bilayer from there, which resulted > in a > large displacement, so I processed the trajectory with trjconv -pbc nojump. > There is still a rather large initial displacement (within the first several > nanoseconds out of 100, likely due to my equilibration procedure of packing > the > lipids tightly around the peptide), so I attempted to analyze the last 75 ns > and > 90 ns of the trajectory, using the structures at those times as the reference > (in g_msd -s). Still the same result, a large value of D. > > Any ideas? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) > > Thanks again. > > -Justin > > > Quoting Alan Dodd <[EMAIL PROTECTED]>: > >> What happens if you visualise the trajectory? Two orders of magnitude in >> scale of lipid movement should stick out like a sore thumb. >> >> - Original Message >> From: Justin A. Lemkul <[EMAIL PROTECTED]> >> To: gmx-users@gromacs.org >> Sent: Wednesday, January 16, 2008 12:27:45 AM >> Subject: [gmx-users] About g_msd >> >> Hello again, >> >> I'm back with a few more questions about g_msd (version 3.3, in case I hadn't >> mentioned that before). Thanks to Xavier's message earlier, I have abandoned >> use of ordered trajectories to analyze my lipids. I will deal with lipid >> "shells" in the future. For now I am approaching the problem of lateral >> diffusion coefficients from a slightly different angle. >> >> My system contains a helical peptide that is oriented asymmetrically with >> respect to the DPPC bilayer. It is tilted and only partially embedded into >> the >> intracellular leaflet of the bilayer (at the beginning of the simulation). >> Due >> to the asymmetry, I would like to study the properties of the leaflets >> separately, including, among other parameters, the lateral diffusion >> coefficients of the component lipids. >> >> I have found a few papers that have simulated pure DPPC bilayers, and am >> using >> them as somewhat of a reference point for the magnitude of the lateral >> diffusion coefficients that I am determining: E. Lindahl and O. Edholm >> (2001) >> J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. >> J. >> 76. >> >> For the top leaflet of my bilayer, I am getting a value of D = >> (4.0+/-2.2)x10^-7 >> cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the >> bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I >> figured >> this enormous number was due to artefacts of PBC, so I tried every iteration >> of >> trjconv -pbc, but to no avail. Every result is quite similar. I tried >> starting g_msd at a later time (10 ns, 25 ns) to determine if any large >> initial >> movements of lipids were responsible for the result, but I'm still coming up >> with the enormous value of D (albeit slightly lower, ~200+/-400) >> >> I am using g_msd -mol, with an index file that contains molecule numbers, and >> then using g_analyze on the output .xvg file to get the values of D. >> >> Has anyone ever experienced anything similar? Am I missing something >> obvious? >> >> Thanks in advance, as always, especially if you read the entirety of my >> lengthy >> message. >> >> -Justin >> >> >> >> >> Justin A. Lemkul >> Graduate Research Assistant >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> [EMAIL PROTECTED] | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> >> >> _
Re: [gmx-users] About g_msd
What happens if you visualise the trajectory? Two orders of magnitude in scale of lipid movement should stick out like a sore thumb. - Original Message From: Justin A. Lemkul <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, January 16, 2008 12:27:45 AM Subject: [gmx-users] About g_msd Hello again, I'm back with a few more questions about g_msd (version 3.3, in case I hadn't mentioned that before). Thanks to Xavier's message earlier, I have abandoned use of ordered trajectories to analyze my lipids. I will deal with lipid "shells" in the future. For now I am approaching the problem of lateral diffusion coefficients from a slightly different angle. My system contains a helical peptide that is oriented asymmetrically with respect to the DPPC bilayer. It is tilted and only partially embedded into the intracellular leaflet of the bilayer (at the beginning of the simulation). Due to the asymmetry, I would like to study the properties of the leaflets separately, including, among other parameters, the lateral diffusion coefficients of the component lipids. I have found a few papers that have simulated pure DPPC bilayers, and am using them as somewhat of a reference point for the magnitude of the lateral diffusion coefficients that I am determining: E. Lindahl and O. Edholm (2001) J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J. 76. For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7 cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I figured this enormous number was due to artefacts of PBC, so I tried every iteration of trjconv -pbc, but to no avail. Every result is quite similar. I tried starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial movements of lipids were responsible for the result, but I'm still coming up with the enormous value of D (albeit slightly lower, ~200+/-400) I am using g_msd -mol, with an index file that contains molecule numbers, and then using g_analyze on the output .xvg file to get the values of D. Has anyone ever experienced anything similar? Am I missing something obvious? Thanks in advance, as always, especially if you read the entirety of my lengthy message. -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] image control
Try using ngmx to visualise the simulation like I said, that'll tell you exactly what bonds gromacs thinks are there and definitively confirm whether there's a problem in the setup. Files that may have caused the problem are of course the obvious things like your mdp (what you've set pbc to, for instance), your topology (have you specified the bonds correctly in the first place?). If it turns out to just be a visualisation problem when using VMD, try using trjconv to dump out the first frame directly as a .gro for VMD. And, of course, using trjconv and specifying an appropriate -pbc option to 'fix' the pbc is something to do. - Original Message From: Myunggi Yi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, January 15, 2008 5:18:58 PM Subject: Re: [gmx-users] image control I don't think this is caused by VMD. The real coordinates of the part of the molicule in the .gro file (restart file from the end of simulation) will tell you. This means gromacs doesn't keep the whole molecule. Would you let me know what simulation setup you need for the cheking? I used editconf to convert the .pdb file to .gro file. Since the structure (.pdb) was pre-equilibrated one, I did setup box size manually (not using editconf). There were more than three float numbers at the bottom of .gro file. I left only the first three, and replaced with the known box size. Is this enough for PBC simulation? (manually typing box size at the bottom of .gro file) On Jan 15, 2008 10:13 AM, Alan Dodd <[EMAIL PROTECTED]> wrote: I'd suggest this is an issue with VMD rather than gromacs. You have to be quite careful which .gro you use to provide the original structure, make sure it is actually the starting frame and not anything else - this is something I've seen cause this sort of problem before. Normally, of course, PBC settings in Gromacs keep molecules whole in the output file quite reliably, but not knowing how you've set your simulation up, I couldn't comment on that. Using ngmx is a good way to check that Gromacs itself is doing what you think it is. - Original Message From: Myunggi Yi < [EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, January 15, 2008 2:51:20 PM Subject: [gmx-users] image control Dear users, I'm running NPT simulation POPC with a short peptide. I see the long bonds across the unit cell in VMD. Why am I getting broken lipid molecules in the trajectory (original .xtc file w/o any post-modification)? Some lipids move whole molecules, but some are broken. How can I control the unit of image? I couldn't find any related word in the manual. I assume image will be done by "residue". Then I shouldn't get this strange result. I got the popc.itp from Dr. Tieleman's web site. Any idea? -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] . Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your homepage. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping__
Re: [gmx-users] image control
I'd suggest this is an issue with VMD rather than gromacs. You have to be quite careful which .gro you use to provide the original structure, make sure it is actually the starting frame and not anything else - this is something I've seen cause this sort of problem before. Normally, of course, PBC settings in Gromacs keep molecules whole in the output file quite reliably, but not knowing how you've set your simulation up, I couldn't comment on that. Using ngmx is a good way to check that Gromacs itself is doing what you think it is. - Original Message From: Myunggi Yi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, January 15, 2008 2:51:20 PM Subject: [gmx-users] image control Dear users, I'm running NPT simulation POPC with a short peptide. I see the long bonds across the unit cell in VMD. Why am I getting broken lipid molecules in the trajectory (original .xtc file w/o any post-modification)? Some lipids move whole molecules, but some are broken. How can I control the unit of image? I couldn't find any related word in the manual. I assume image will be done by "residue". Then I shouldn't get this strange result. I got the popc.itp from Dr. Tieleman's web site. Any idea? -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_density
Atoms. - Original Message From: Antonia Vyrkou <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, January 8, 2008 4:05:26 PM Subject: [gmx-users] g_density Dear all, When using the g_density tool am I calculating the density of a group of molecules in respect to the atoms or to the center of mass of these molecules? Thank you for your help Antonia Sent from Yahoo! - a smarter inbox. -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in bilayer simulation
I'm going to assume you've read http://wiki.gromacs.org/index.php/Doing_Restarts. I suggest you also look more closely at the manual page for trjconv. - Original Message From: pragya chohan <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, December 31, 2007 1:56:41 PM Subject: RE: [gmx-users] problem in bilayer simulation I think you misunderstood my reply. I understood that it is a periodic boundry condition problem and used trjconv. But it writes a trajectory file. How do I make a gro file to input it into next run? I cant even use tpbconv command because trjconv writes a xtc file and I need a trr file for my next run? > Date: Mon, 31 Dec 2007 08:17:15 +1100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] problem in bilayer simulation > > pragya chohan wrote: > > Dear Users > > I am doing membrane simulation alternating nvt and npt during production > > run. After 1250 ps the water from upper leaflet goes towards the lower > > leaflet and a very thin layer of water remains in the upper leaflet. Is > > it a common occurance or am I doing some mistake? > > Probably you are observing an artefact of periodic boundary conditions - > see http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions for > advice here. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Post free property ads on Yello Classifieds now! www.yello.in http://ss1.richmedia.in/recurl.asp?pid=221___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in pr.mdp file
What's the difference between the two runs? Isolate which of the differences makes your simulation run slow, and then the answer might present itself. - Original Message From: sudheer <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, December 31, 2007 12:20:48 PM Subject: [gmx-users] problem in pr.mdp file hi gromacs users, iam getting problem while doing postion restrian for the protein system reunning very slow, but i have done md.mdp for another system( bilayer-popc) its running normally, whats the problem in my protein system? i have used pr.mdp file like i am enlosing along with my mail User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 nsteps = 25000 nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 pbc = xyz ; Berendsen temperature coupling is on in two groups ; Pressure coupling is on Tcoupl = berendsen tc-grps = Protein SOLNa+ tau_t = 0.1 0.10.1 ref_t = 300 300300 Pcoupl = parrinello-rahman pcoupltype = isotropic ref_p = 1 tau_p = 0.5 compressibility = 4.5e-5 ; Energy monitoring energygrps = Protein SOL Na+ ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 41,1 Bot 3,1 Top pls help me in this problem -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in bilayer simulation
Does the water move through the bilayer, or is this a PBC thing? It sounds like your bilayer is translating upwards? - Original Message From: pragya chohan <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Sunday, December 30, 2007 3:25:51 PM Subject: [gmx-users] problem in bilayer simulation Dear Users I am doing membrane simulation alternating nvt and npt during production run. After 1250 ps the water from upper leaflet goes towards the lower leaflet and a very thin layer of water remains in the upper leaflet. Is it a common occurance or am I doing some mistake? Please help Live the life in style with MSN Lifestyle. Check out! Try it now! -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] image centering
Have you tried running trjconv with -centre (selecting SOL, obviously), and then running trjconv -pbc on the result? I have a vague memory of finding seperating the commands gives a different result, as if the two options were interfering with each other. What does the output look like when you use the option -centre? If nothing else, seperating the commands might help you find the source of the problem. - Original Message From: Myunggi Yi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, December 25, 2007 9:48:29 PM Subject: [gmx-users] image centering Dear users, I have a membrane simulation trajectory, in which the solvent (water and ions) is separated by lipid bilayer. I want to center the solvent so that the membrane is separated by two layers at the bottom and top in the unit cell. I have tried the followings. trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -n ../memb.ndx -pbc cluster trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -s ../Eq9/eq9.gro -n ../memb.ndx -center rect -pbc whole Both pbc and center didn't work. Is there any way to center the solvent? Happy holidays. -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] membranes & proteins revisited
Of course it's unnatural, it's a membrane made of gas instead of lipid ;) I'd recommend that you equilibrate the "membrane" first, and check it actually behaves in a manner close enough to one for what you want - and then insert a protein into it. You might want to look into the make_hole suite on the user contributions page, it's designed to make a hole in a lipid membrane for a protein, but I'm sure modifying it for argon would be rather trivial. - Original Message From: Magnus Andersson <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, December 18, 2007 9:38:09 PM Subject: [gmx-users] membranes & proteins revisited Hi all, I have a trimer membrane protein structure & an artificial Argon grid membrane (100x100x30Å). First I wonder whether you should equilibrate the membrane first (it looks very un-natural, like a perfect grid...) and then physically remove atoms where I want to have my protein, then run: genbox -cp protein.gro -cs membrane.gro if I just run it as it is, I get: Checking Protein-Solvent overlap: tested 1512 pairs, removed 9261 atoms. I feel I'm getting there, but need some advice to come to the point where I have my trimer in a "relaxed" membrane... Thanks / Magnus -- Magnus Andersson Chalmers University of Technology Dept of Chemistry and Biological Engineering Email: [EMAIL PROTECTED] Homepage: http://www.csb.gu.se/neutze/ Phone: +46 (0)31-786 3917 Fax: +46 (0)31-786 3910 Lundberg Laboratory Medicinaregatan 9e SE-413 90 Göteborg Sweden ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
What topology are you using? If you're using one based on the Kartunnen's group POPG (the only publicly available one I know of), then be aware that I think they saw gel phase too. Oh, and read the email you replied to, particularly the bit about 18 angstroms. - Original Message From: Myunggi Yi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, December 13, 2007 6:48:20 PM Subject: Re: [gmx-users] Gel Phase in DMPC using Berger force field ?? I'm running MD at 300 K. I want fluid phase. On 12/13/07, Myunggi Yi <[EMAIL PROTECTED]> wrote: Dear Eric, I'm using Berger force field for DOPG (anionic head group). Is is true for DOPG also? The following is my MD input. I'm getting smaller area per lipid (~52 A^2) than expected (~62). What should I change? ** ; nblist cut-off rlist= 1.6 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.6 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 1.2 rvdw = 1.4 ** On 12/11/07, Eric Jakobsson <[EMAIL PROTECTED] > wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: >Hi Steffen, > >thanks a lot for your reply. >>-what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm >>twin range cutoff for working properly. Are you using PME for >>electrostatics? >> >I used a LJ-cutoff at 1.0nm. That's what was >used for the original Berger-Paper (*O Berger, O >Edholm and F Jähnig, */Biophysical Journal/ 72: >2002-2013 (1997). Shouldn't this be all right? > >And I used PME (which was indeed not used in the original work. > >>-how did you set up the pressure coupling? >> >I used weak coupling (tau=1.0ps) > >>-900 waters are not really much, the head groups will probably interact >>with their mirror images due to pbc. Try a lot more (thought about >>1?) for having a "real" bilayer in a solution. >> >I also tried with more water, the gel phase did not appear either. > >> >From my experience, the Berger lipids are well defined for a specific >>temperature, but if you go up/down the temperature scale, they are not >>really following the experimental values/phase behaviour. By the way: >>experimental data on lipid order parameters varies considerably >>throughout the complete literature, so don't rely onto that too much as >>well. >>Sorry for giving more questions than answers, but that's the shitty part >>with lipid bilayers in MD... >>Steffen >> >Thanks again, >Jochen > > > >-- > >Jochen Hub >Max Planck Institute for Biophysical Chemistry >Computational biomolecular dynamics group >Am Fassberg 11 >D-37077 Goettingen, Germany >Email: jhub[at]gwdg.de > >___ >gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! >Please don't post (un)subscribe requests to the >list. Use the www interface or send it
Re: [gmx-users] Recover velocity from trr file and coordinates from xtc file
You need full precision coordinates (i.e. trr and not xtc) for an accurate restart. You might be able to bodge it with the use of trjconv/trjcat or something to make a "pretend" trr with coordinates and velocities, but I wouldn't count on it. Oh, and a restart file is a tpr, not a gro. Making a .gro file is easy - see manual page on trjconv. The manual is useful. - Original Message From: Myunggi Yi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Friday, November 30, 2007 3:54:17 PM Subject: Re: [gmx-users] Recover velocity from trr file and coordinates from xtc file Thank you for your help. However, I can't understand how to generate gro file from trr and xtc files. I'm sorry. I'm a beginner. Would you let me know exact command? or where can I find? Again, I saved velocity only in trr file, and I have xtc file (only coordinates). I have edr file also. I found the following to make the restart file (gro file). tpbconv -s eq5.tpr -f eq5.trr -e eq5.edr -o eq6.tpr -time 6870.000 Since I have velocity only in the trr file, I can't apply this. Any idea? On Nov 29, 2007 11:17 AM, Alan Dodd < [EMAIL PROTECTED]> wrote: > http://wiki.gromacs.org/index.php/Doing_Restarts > > You can make a gro with what you have. You *may* be able to continue your > run properly. Read the above link. > > > - Original Message > From: Myunggi Yi <[EMAIL PROTECTED]> > To: gmx-users@gromacs.org > Sent: Thursday, November 29, 2007 4:06:06 PM > Subject: [gmx-users] Recover velocity from trr file and coordinates from xtc > file > > Dear Gmx users, > > Can I make a gro file (restart file) from trr (I saved only velocities) > and xtc file (which has the coordinates)? > If I can, how can I do this job? > I'm a beginner. > > Have a nice day. > > > > -- > Best wishes, > > MYUNGGI YI > == > KLB 419 > Institute of Molecular Biophysics > Florida State University > Tallahassee, FL 32306 > > Office: (850) 645-1334 > http://www.scs.fsu.edu/~myunggi > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > Never miss a thing. Make Yahoo your home page. > http://www.yahoo.com/r/hs > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Recover velocity from trr file and coordinates from xtc file
http://wiki.gromacs.org/index.php/Doing_Restarts You can make a gro with what you have. You *may* be able to continue your run properly. Read the above link. - Original Message From: Myunggi Yi <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Thursday, November 29, 2007 4:06:06 PM Subject: [gmx-users] Recover velocity from trr file and coordinates from xtc file Dear Gmx users, Can I make a gro file (restart file) from trr (I saved only velocities) and xtc file (which has the coordinates)? If I can, how can I do this job? I'm a beginner. Have a nice day. -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] area by lipid
- Original Message From: maite lopez cabezas <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Sunday, November 25, 2007 10:48:31 AM Subject: Re: [gmx-users] area by lipid Well I know that the x/y directions are scaled isotropically and the z direction is scaled independiently, and i must give just 2 compresibility valors, but people don't give this valor in the most of the papers about membrane simulations. For example i use on DPPC membrane compressibility =4.5e-5 4.5e-5 ref-p= 1.0 1.0 the area change from 0.64 to 0.62. When i use the same parameter on POPG or POPC bilayer the system is exploding. If i change to on POPC and POPG compressibility =1.0e-5 4.5e-5 ref-p= 1.0 1.0 it gives areas about 0.639 (POPC) and 0.53 (POPG). The POPG area is according to "Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions", W. Zhao, T. Rog, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, Biophys J. 92, 1114-1124 (2007), and I'm using the same temperature. But the POPC area isn't good. -> Is that the POPG where they observe a permanent hydrogen bond between the mid-OH of the glycerol, and the phosphate? My questions are: Can i use compressibility =0 4.5e-5 and ref-p = 0 1.0 on peptide-membrane systems? (at first the peptide is about 10 A to the bilayer interface and after it's inserting in the membrane) -> Not unless you *intend* the membrane to be unable to expand or contract. This is what gave you zero variability before. Compressibility of zero means your box will not compress (or expand) in that dimension. If you're adding peptides, I'd imagine true NPT is important. Personally, I use a surface tension (XY pressure not equal to 1) to artificially fix the area/lipid. This still has issues, of course... What are the correct valors for the compressibility on membrane systems? -> People don't tend to specify in their papers, unfortunately. I've always gone for using the water value, as it'll be in the right ballpark and I don't believe it's too critical. Thanks a lot, Maité On Nov 24, 2007 10:27 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > > Hi: > > > > I am working on membrane simulation under lipid (DPPC, from Peter > > Tieleman group site). I equilibrated dppc membrane for 10 ns and when > > i got the area by lipid (x*y/ # lipids) using g_energy, i obtained > > that the area is constant (0.64), there isn't any fluctuaction during > > 10 ns..althougth the volumen isn't constant. > > What's wrong in this simulation? > > Did you notice that your box dimensions are not changing in X and Y > directions? Do you understand what semiisotropic pressure coupling does? > > Mark > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] area by lipid
Yes. Compressibility of 0 for X/Y dimensions would tend to result in a static (i.e., non-compressible!) box. Look for some papers on lipid simulations - excessively low area/headgroup is a common problem, and there are a variety of opinions on how to approach this. - Original Message From: maite lopez cabezas <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Sunday, November 25, 2007 12:02:22 AM Subject: Re: [gmx-users] area by lipid Thanks Alan I tried with traj too and it's the same resultsomebody use g_energy or g_traj. The cuestion is having x and y. The problem is I want to simulated a peptide-membrane system and the area couldn't be constant cause the insertion of the peptide increases the bilayer area. I think that is the compressibility , i changed my parameters from compressibility = 0 4.5e-5 ref-p= 0 1.0 to compressibility =4.5e-5 4.5e-5 ref-p= 1.0 1.0 and the area changed from 0.645 to 0.62 and it isn't a good valor. Maite These the output traj -ob # g_traj_331 -ob box.xvg -f dppc128_3ns_ok.xtc -e 1000 -s 3.tpr -nice 0 # # g_traj_331 is part of G R O M A C S: # # Grunge ROck MAChoS # @title "Box vector elements" @xaxis label "Time (ps)" @yaxis label "(nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "XX" @ s1 legend "YY" @ s2 legend "ZZ" @ s3 legend "YX" @ s4 legend "ZX" @ s5 legend "ZY" 0 6.3696 6.3998 6.680 0 0 1 6.3696 6.3998 6.64996 0 0 0 2 6.3696 6.3998 6.63114 0 0 0 3 6.3696 6.3998 6.60618 0 0 0 4 6.3696 6.3998 6.59534 0 0 0 5 6.3696 6.3998 6.5969 0 0 0 6 6.3696 6.3998 6.58594 0 0 0 7 6.3696 6.3998 6.57235 0 0 0 8 6.3696 6.3998 6.57301 0 0 0 9 6.3696 6.3998 6.55283 0 0 0 10 6.3696 6.3998 6.5441 0 0 0 11 6.3696 6.3998 6.52643 0 0 0 12 6.3696 6.3998 6.54106 0 0 0 13 6.3696 6.3998 6.53806 0 0 0 14 6.3696 6.3998 6.54126 0 0 0 15 6.3696 6.3998 6.53768 0 0 0 On Nov 24, 2007 6:00 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > I didn't think g_energy was useful for that - I've always used g_traj -ob to > get box dimensions. If noone has a better answer, you should probably just > try that and see if you get the same effect. > > > - Original Message > From: maite lopez cabezas <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Sent: Saturday, November 24, 2007 10:01:24 PM > Subject: [gmx-users] area by lipid > > > Hi: > > I am working on membrane simulation under lipid (DPPC, from Peter > Tieleman group site). I equilibrated dppc membrane for 10 ns and when > i got the area by lipid (x*y/ # lipids) using g_energy, i obtained > that the area is constant (0.64), there isn't any fluctuaction during > 10 ns..althougth the volumen isn't constant. > What's wrong in this simulation? > Any help will be highly appreciated. Thanks > > Maite > > > These g_energy output: > -- > @ legend length 2 > @ s0 legend "Kinetic-En." > @ s1 legend "Total-Energy" > @ s2 legend "Temperature" > @ s3 legend "Pressure-(bar)" > @ s4 legend "Box-X" > @ s5 legend "Box-Y" > @ s6 legend "Box-Z" > @ s7 legend "Volume" > @ s8 legend "Density-(SI)" > @ s9 legend "T-DPP" > @ s10 legend "T-SOL" >0.00 44884.128906 -299551.125000 309.756866 -2867.529297 > 6.3696006.3998006.68 272.304596 974.509155 312.786591 > 307.970825 >20.00 44859.781250 -252572.656250 309.588837 62.661823 > 6.3696006.3998006.516144 265.625153 999.014282 310.579834 > 309.004639 >40.00 44840.101562 -252600.875000 309.453064 -93.168358 > 6.3696006.3998006.494525 264.743896 1002.339722 306.650665 > 311.105103 >60.04 45093.398438 -253077.312500 311.20 -99.019768 > 6.3696006.3998006.491228 264.609497 1002.848877 310.111328 > 311.843567 >80.00 45020.613281 -252663.734375 310.698822 19.632711 > 6.3696006.3998006.504295 265.142151 1000.834167 309.710663 > 311.281342 > 100.08 44901.433594 -252496.687500 309.876312 122.716400 > 6.3696006.39980
Re: [gmx-users] area by lipid
I didn't think g_energy was useful for that - I've always used g_traj -ob to get box dimensions. If noone has a better answer, you should probably just try that and see if you get the same effect. - Original Message From: maite lopez cabezas <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Saturday, November 24, 2007 10:01:24 PM Subject: [gmx-users] area by lipid Hi: I am working on membrane simulation under lipid (DPPC, from Peter Tieleman group site). I equilibrated dppc membrane for 10 ns and when i got the area by lipid (x*y/ # lipids) using g_energy, i obtained that the area is constant (0.64), there isn't any fluctuaction during 10 ns..althougth the volumen isn't constant. What's wrong in this simulation? Any help will be highly appreciated. Thanks Maite These g_energy output: -- @ legend length 2 @ s0 legend "Kinetic-En." @ s1 legend "Total-Energy" @ s2 legend "Temperature" @ s3 legend "Pressure-(bar)" @ s4 legend "Box-X" @ s5 legend "Box-Y" @ s6 legend "Box-Z" @ s7 legend "Volume" @ s8 legend "Density-(SI)" @ s9 legend "T-DPP" @ s10 legend "T-SOL" 0.00 44884.128906 -299551.125000 309.756866 -2867.529297 6.3696006.3998006.68 272.304596 974.509155 312.786591 307.970825 20.00 44859.781250 -252572.656250 309.588837 62.661823 6.3696006.3998006.516144 265.625153 999.014282 310.579834 309.004639 40.00 44840.101562 -252600.875000 309.453064 -93.168358 6.3696006.3998006.494525 264.743896 1002.339722 306.650665 311.105103 60.04 45093.398438 -253077.312500 311.20 -99.019768 6.3696006.3998006.491228 264.609497 1002.848877 310.111328 311.843567 80.00 45020.613281 -252663.734375 310.698822 19.632711 6.3696006.3998006.504295 265.142151 1000.834167 309.710663 311.281342 100.08 44901.433594 -252496.687500 309.876312 122.716400 6.3696006.3998006.506715 265.240784 1000.461975 312.459656 308.353394 120.08 44964.890625 -252896.796875 310.314270 -124.685959 6.3696006.3998006.514557 265.560486 999.257568 306.510254 312.556793 140.00 45168.968750 -252813.281250 311.722626 -290.249481 6.3696006.3998006.488441 264.495850 1003.279724 312.059570 311.524017 160.00 44465.328125 -253265.328125 306.866638 368.317017 6.3696006.3998006.500315 264.979919 1001.446960 307.570343 306.451813 180.15 44680.867188 -252064.906250 308.354126 -243.635345 6.3696006.3998006.491784 264.632141 1002.763062 309.213043 307.847809 200.15 44827.578125 -252667.828125 309.366638 -166.550201 6.3696006.3998006.477999 264.070221 1004.896851 308.571106 309.835602 220.15 44968.542969 -253124.671875 310.339447 -171.839508 6.3696006.3998006.487612 264.462097 1003.407837 309.458679 310.858673 240.15 44708.015625 -253120.671875 308.541504 203.768204 6.3696006.3998006.498459 264.904236 1001.733032 307.988251 308.867645 2.. - These is my .mdp file - ; VARIOUS PREPROCESSING OPTIONS title= DM com Restricoes cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 150 ; = 3000.0 ps ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 1000 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 5 nstvout = 5 nstfout = 5 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 10 ; Output f
Re: Re: [gmx-users] trjconv does not work
The length of your simulation is irrelevant, the frequency of frame output is. If you don't output frames at least 5x per picosecond, asking for the frames in a 0.1ps gap is not going to produce an output - because there probably won't be any. Check your mdp. - Original Message From: OZGE ENGIN <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Cc: gmx-users@gromacs.org Sent: Monday, November 19, 2007 5:12:51 PM Subject: Re: Re: [gmx-users] trjconv does not work Of course, I am performing a 40 ns simulation, and 14 ns of it has been finished. What may be the problem? I know, I can extract specific frames via VMD, but it changes atom types after saving in pdb format. -Original Message- From: Ran Friedman <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Mon, 19 Nov 2007 17:53:16 +0100 Subject: Re: [gmx-users] trjconv does not work I see. Do you have any structure between t=0.1ps and t=0.2ps? Ran. OZGE ENGIN wrote: > The command line ws the following: > > trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] combining gromos96 (43a2) and berger lipid force field
The quick answer would be to look at the ffgmx forcefield, and the ffgmx/Berger hybrid that can be obtained (either from Tieleman or the Gromacs website, I forget) and work out how the former was incorporated into the latter. Then replicate that for ffG43a2. Not necessarily simple or even valid, but that's MD for you. - Original Message From: maria goranovic <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, November 7, 2007 7:24:11 PM Subject: [gmx-users] combining gromos96 (43a2) and berger lipid force field I want to use the gromos96 force field for the protein, and Tieleman's Berger force field for the lipids. How do I combine force fields or construct a topology. I have different topologies for the lipids and the protein ready. However combining them would probably lead to errors as I cannot include both the ffG43a2 and the ffgmx force fields in the same topology ? Thanks for the help, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with waters in protein/membrane simulation
You can play with mdrun_hole (search the site) which is designed to create a protein-shaped hole in a lipid simulation (also making a hole in the water). I'd probably just delete the offending waters, and reequilibrate, myself. - Original Message From: N-J.M. Macaluso <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, November 6, 2007 2:11:47 PM Subject: [gmx-users] problem with waters in protein/membrane simulation Hello, I'm having a small but significant problem with simulating a protein inserted in a DPPC membrane. I have simulated the system for 15 ns with position restraints on the protein to allow the lipids to anneal around it, but have recently found a small problem. I found a small gap between the protein and lipid where some water molecules embedded themselves. Is there any way I can change the parameters of the simulation to remove these waters, so that the lipids will aggregate properly around the protein? What would the best solution be? Should I just remove these waters manually? Thanks, Max Macaluso ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Regarding Box-X Box-Y values from g_energy
Did you perhaps use semiisotropic pressure coupling? I'd expect the X-Y values to be the same for that. - Original Message From: Sona Aramyan <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, November 1, 2007 1:18:07 PM Subject: [gmx-users] Regarding Box-X Box-Y values from g_energy Dear gmx-users I have a system consisting from 128dppc bilayer which I've took from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) and 1 molecule of DALA. I have 2ns run of it. In my g_energy output energy.xvg, in which I have Box-X Box-Y Box-Z values, the values of Box-X and Box-Y at every step of time have exactly same values. How can this two values change with the same quantity? Is this a real problem, can I use the results of the it or something is wrong with this simulation? I'm sending to you a part of my energy.xvg Any suggestions and advises will be very very appreciated. # This file was created by g_energy # which is part of G R O M A C S: # Gnomes, ROck Monsters And Chili Sauce # All this happened at: Thu Oct 25 15:12:53 2007 # @title "Gromacs Energies" @xaxis label "Time (ps)" @yaxis label "E (kJ mol\S-1\N)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Box-X" @ s1 legend "Box-Y" @ s2 legend "Box-Z" 0.006.3437206.3437206.777830 4.006.2796316.2796316.709337 8.006.2465506.2465506.673972 12.016.2916966.2916966.722235 16.006.2744856.2744856.703831 20.006.2596736.2596736.688022 24.026.2744586.2744586.703805 28.026.2690536.2690536.698055 32.006.2730666.2730666.702339 36.006.2777206.2777206.707294 40.006.2684056.2684056.697363 44.046.2621656.2621656.690718 48.046.2715166.2715166.700673 52.046.2829006.2829006.712825 56.046.2680046.2680046.696920 60.046.2759516.2759516.705416 64.006.2839906.2839906.713978 68.006.2683326.2683326.697258 72.006.2686726.2686726.697591 76.006.2820326.2820326.711858 80.006.2759106.2759106.705327 84.086.2719636.2719636.701087 88.086.2719786.2719786.701059 92.086.2659826.2659826.694634 96.086.2727396.2727396.701852 100.086.2709916.2709916.699977 104.086.2593236.2593236.687513 108.086.2655846.2655846.694173 112.086.2692796.2692796.698182 116.086.2675906.2675906.696383 120.086.2663726.2663726.695080 124.086.2572706.2572706.685329 128.006.2637626.2637626.692231 132.006.2721916.2721916.701218 136.006.2662366.2662366.694935 140.006.2612526.2612526.689645 144.006.2594186.2594186.687694 148.006.2687996.2687996.697742 152.006.2742106.2742106.703519 156.006.2698866.2698866.698938 160.006.2733046.2733046.702565 164.156.2702556.2702556.699334 168.156.2797716.2797716.709496 172.156.2710506.2710506.700203 176.156.2585786.2585786.686853 180.156.2698286.2698286.698884 184.156.2763796.2763796.705905 188.156.2600806.2600806.688455 192.156.2616066.2616066.690063 196.156.2757626.2757626.705174 200.156.2636846.2636846.692267 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] angle between helices
g_bundle does give the angle between helix pairs...? Not directly, admittedly, but it gives you the tilt from the main axes, which you can use with some basic math to work out the angle between helices. - Original Message From: Anupam Nath Jha <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, October 29, 2007 10:37:13 AM Subject: Re: [gmx-users] angle between helices HI David there are options like g_helix, g_angle and as you said g_bundle, but none of them gives the angle between helix pairs. anupam > Marc F. Lensink wrote: >> On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: >>> Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? >>> Probably. Check out section 7.4 of the manual. >> >> i wrote a program for that. contact me off-list. >> >> as soon as i find a free moment, i'll upload it to the contrib page. >> > otherwise g_bundle might do it > >> cheers, >> marc >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] forcefield validation
Use the topologies/forcefields in a simulation/energy minimisation, and check that any predictions made by the simulation match up with any available experimental evidence. Hopefully, you'll see that predictions are confirmed by existing experiments, and will suggest new experiments to be done. - Original Message From: Qin Shanshan <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, October 16, 2007 2:48:44 PM Subject: [gmx-users] forcefield validation Dear gms-users, I have a fundamental question to put forward. If I want to construct a forcefield for an organic molecule of middle size,which has about 100 atoms, how can I prove that my forcefield for this molecule is correct? Althouth we can get ffgmx itp files from prodrg server, can we be sure that these topologies are definitely correct? If we want to convince others that our topologies are right, is there any criteria to compare with? If I want to derive a forcefield for a particular molecule, what should I do? Any suggestion will be appreciated, thanks very much in advance. Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] anisotropic pressure coupling for temperature annealing
Have you simulated the system without the annealing, to see if it does the same thing? Bilayers are very sensitive to minor changes in setup, using someone else's equilibrated bilayer coordinates doesn't mean it's equilibrated for your system. - Original Message From: Q733 <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, October 10, 2007 6:40:06 AM Subject: [gmx-users] anisotropic pressure coupling for temperature annealing Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y dimension increased with time in the whole procedure, but actually the area/lipid should decrease when tempreture decreases. I think there may due to the P couple parameters I used. Now I write them here: tau_p = 2.0 2.0 2.0 0 0 0 compressibility = 4.5e-6 4.5e-6 4.5e-6 0 0 0 ref_p = 11 1 1 1 1 Is there anything wrong with my parameter? or should I use ref_p = 11 1 0 0 0 I saw someone use this ref_p before. Any suggestion will be appreciated, thanks in advance. Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get listings, and more! http://tv.yahoo.com/collections/3658 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to change the box size during simuation
You can apply external forces to subsets of atoms, in such a way as to cause your box to shrink by itself. - Original Message From: WU Yanbin <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, October 9, 2007 11:40:21 PM Subject: [gmx-users] How to change the box size during simuation Hey, Now I'm simulating infinite molecules. I want to change the box size a lit bit every time step so as to induce some stress in this system. Is there any way in gromacs to do this, apart from modifying the code? Thanks in advance. Yours Sincerely, WU Yanbin Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] only one cpu "works" in my linux cluster
Yeah. Check the machinefile tells mpich what you think it does. It looks pretty certain to be an issue with mpich rather than gromacs. Unfortunately, I don't use mpich any more because I find LAM better. Standard procedure, turn up the verbosity on everything, check the outputs, re-read the relevant manuals. - Original Message From: liu xin <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, October 9, 2007 1:38:50 PM Subject: Re: [gmx-users] only one cpu "works" in my linux cluster Thanks Alan in fact I've already added the option -machinefile, here's the script: cat $PBS_NODEFILE >/home/liuxin/mpd.hosts /home/liuxin/mpich2/bin/mpdboot -n 6 -f mpd.hosts /home/liuxin/mpich2/bin/mpiexec -machinefile $PBS_NODEFILE -np 12 /home/liuxin/ programs/gromacs33mpi/bin/mdrun -v -s 12np.tpr -o -c -e -g -np 12 I am a little busy today, sorry for replying so late... On 10/8/07, Alan Dodd <[EMAIL PROTECTED]> wrote: Check the MPICH manuals for how to specify the nodes to run on. From memory, the option -machinefile lets you do this. - Original Message From: liu xin < [EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, October 8, 2007 1:51:12 PM Subject: [gmx-users] only one cpu "works" in my linux cluster Dear GMXers this is how I've done it so far: grompp -f -c -p -o 12np.tpr -np 12 qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s 12np.tpr -np 12 ) then it seems my mdrun works fine, but when I ssh to each node to check the cpu efficiency with "top", I find that there's only one cpu works with 12 processes! The other nodes are completely idle. the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux our administrator have installed mpich1.2.7 in the default DIR (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so I installed mpich2 in my personal dir. I've searched the list, but cant get any solution. Does it have something to do with the kernel or there's some conflict between mpich1 and 2, or something else? This is the first time I build up a Linux Cluster on my own, ANY suggestions are appreciated ! Xin Liu Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Check out the hottest 2008 models today at Yahoo! Autos. http://autos.yahoo.com/new_cars.html___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] only one cpu "works" in my linux cluster
Check the MPICH manuals for how to specify the nodes to run on. From memory, the option -machinefile lets you do this. - Original Message From: liu xin <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, October 8, 2007 1:51:12 PM Subject: [gmx-users] only one cpu "works" in my linux cluster Dear GMXers this is how I've done it so far: grompp -f -c -p -o 12np.tpr -np 12 qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s 12np.tpr -np 12 ) then it seems my mdrun works fine, but when I ssh to each node to check the cpu efficiency with "top", I find that there's only one cpu works with 12 processes! The other nodes are completely idle. the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux our administrator have installed mpich1.2.7 in the default DIR (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so I installed mpich2 in my personal dir. I've searched the list, but cant get any solution. Does it have something to do with the kernel or there's some conflict between mpich1 and 2, or something else? This is the first time I build up a Linux Cluster on my own, ANY suggestions are appreciated ! Xin Liu Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Pbc and Com in simulation video
I believe I got as far as determining that the frame coordinates were stored in the rvec fr.x after being read, and passed to do_fit. That rvec structure would be the key to achieving what you want, I guess. When I got to about that point, I decided I could handle a little bobbing about when watching trajectories ;) Alan. - Original Message From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, September 26, 2007 11:27:14 AM Subject: [gmx-users] Re: Pbc and Com in simulation video Thanks for your help Alan, Yang, and Belquis! Now I managed to get trajectory in which a droplet stays in the middle of the simulation box while a surface moves below the droplet. First I used trjconv to remove periodicity (-pbc nojump) and then performed translational fit for the droplet (-fit translational) and finally transferred all the translating surface atoms back to the simulation box (-pbc -inbox). However, there is still a problem with fitting procedure which is performed in three dimension and hence the surface translates upwards during the video. It should be quite easy to modify trjconv so that the fitting is performed only for the xy coordinates (not for the z coordinate perpendicular to the surface) but with my programming skills I wasn't able to do that (actually I wasnt able to find the correct lines). So I would like to know if someone has made a such modification to trjconv (trjconv_d) or could help me to do it? Thanks, Janne > Hello Janne, > > this is what I usually do when my molecules cross the box or dance all > around and it works for me: > > I first do this with the "original" unmodified or fitted xtc or trr file: > > trjconv -f -o -pbc nojump > > then i take the modified trr or xtc and do a fit: > > trjconv -f -s -fit rot+trans > > > Belquis > > >> Hello gmx-users! >> >> I am trying to make a simulation video in which a water droplet is >> rolling or sliding on a surface. Due to a periodic boundary conditions >> a droplet is not whole all the time but it disappears from the right >> and appears from the left in cycles. >> >> I think that I could create more visual video by removing the lateral >> motion of the center of mass of a droplet so that the droplet would >> stay whole >> in the middle of simulation window and the surface would translate >> below the droplet. I am not exactly sure how realistic this kind of >> video would be and would like to know if someone has better ideas? >> >> If there are no better ideas I would need advices to be able to create >> a such trajectory or video. Right now I am struggling with trjconv >> which might be suitable for this purpose. However, if I use the >> droplet as a group for translational fit (-fit translation) I get >> trajectory in which the whole system wanders strangly (laterally (the >> surface moves first to the left and then back to the right) and also >> in perpendicular to the surface due to the lowering of the height of >> the center of mass of the droplet during the simulation) and the >> droplet wont stay whole in the middle of the box. Any ideas what I am >> doing wrong or how I would be able to get rid of even this lateral >> wandering so that I could at least see how realistic this procedure is? >> >> >> Thanks for your time and help in advance, >> >> Janne >> >> >> -- >> Janne Hirvi, MSc(Physical Chemistry), Researcher >> University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, >> FI >> Tel: +358 13 2514544 & +358 50 3474223 >> E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED] >> -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase. http://farechase.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pbc and Com in simulation video
Yes, I know what you mean - I keep meaning to make a modified trjconv where '-fit trans' only affects the xy coordinates, for my bilayers, but it never quite seems important enough. If your droplet moves at a constant rate, trjconv -shift will, I think, move the coordinates by an amount proportional to the framenumber (so at a constant speed) and then all you'd have to do is play with the periodicity. Never tried it though. If you're making the movie with VMD (unpretty, but functional) you can control the periodic imagery quite well in a manner that may help. - Original Message From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, September 25, 2007 4:03:17 PM Subject: [gmx-users] Pbc and Com in simulation video Hello gmx-users! I am trying to make a simulation video in which a water droplet is rolling or sliding on a surface. Due to a periodic boundary conditions a droplet is not whole all the time but it disappears from the right and appears from the left in cycles. I think that I could create more visual video by removing the lateral motion of the center of mass of a droplet so that the droplet would stay whole in the middle of simulation window and the surface would translate below the droplet. I am not exactly sure how realistic this kind of video would be and would like to know if someone has better ideas? If there are no better ideas I would need advices to be able to create a such trajectory or video. Right now I am struggling with trjconv which might be suitable for this purpose. However, if I use the droplet as a group for translational fit (-fit translation) I get trajectory in which the whole system wanders strangly (laterally (the surface moves first to the left and then back to the right) and also in perpendicular to the surface due to the lowering of the height of the center of mass of the droplet during the simulation) and the droplet wont stay whole in the middle of the box. Any ideas what I am doing wrong or how I would be able to get rid of even this lateral wandering so that I could at least see how realistic this procedure is? Thanks for your time and help in advance, Janne -- Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 & +358 50 3474223 E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED] -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ffgmx_lipids.tar.gz
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies should have roughly what you want. Failing that, google is your friend. - Original Message From: Rina Ghosh <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, September 17, 2007 1:12:05 PM Subject: [gmx-users] ffgmx_lipids.tar.gz Hi, I want to perform simulation of membrane protein . I try to downloaded the ffgmx_lipids from : http://www.gromacs.org/topologies/uploaded_force_fields/ffgmx_lipids.tar.gz But, corresponding webpage shows error, URL was not found. Plz attatch this files to my e-mail . I have another question. What force field have I to use . Plz send ffgmx_lipids files to me. Did you know? You can CHAT without downloading messenger. Click here Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] make_ndx and residue name length
Thanks... I think I'll just get the CVS make_ndx and integrate that into my current CVS copy, rather than try to hunt the different locations down! - Original Message From: Berk Hess <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, September 5, 2007 11:22:15 AM Subject: RE: [gmx-users] make_ndx and residue name length >From: Alan Dodd <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] make_ndx and residue name length >Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT) > >The maximum permissible residue name length is at least 5 characters long >for a tpr or gro, but the length of residue name permitted by make_ndx is >only 4 characters. And of course, pdb should have only 3 characters. >While I can change the names in a gro or a pdb quite quickly and easily, is >there a way to change this in a tpr? I'm currently getting around the >problem by converting tprs to pdbs for use by make_ndx, but it's messy... >Alternatively, is there any fundamental reason why the string in make_ndx >inputs is less than that for files, or can I safely bump up the relevant >digit in the code and recompile? I did not know about this check, but now that I have looked at the code it seems I have programmed it myself a decade ago. The only reason for a limit was/is programming convenience. You can change it and recompile, but be careful that the number 5 occurs at multiple places in make_ndx.c I was too lazy to remove the limit, so I have set it to 30 now in the CVS (and also put defined this number in one place only). Berk. _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] make_ndx and residue name length
The maximum permissible residue name length is at least 5 characters long for a tpr or gro, but the length of residue name permitted by make_ndx is only 4 characters. And of course, pdb should have only 3 characters. While I can change the names in a gro or a pdb quite quickly and easily, is there a way to change this in a tpr? I'm currently getting around the problem by converting tprs to pdbs for use by make_ndx, but it's messy... Alternatively, is there any fundamental reason why the string in make_ndx inputs is less than that for files, or can I safely bump up the relevant digit in the code and recompile? Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Unusual structures generated by GENCONF command and resultant minimization problem
Capping peptides is non-trivial, so the error may have been introduced there - certainly the approach you stated is not what I or others have used successfully. There have been a number of posts discussing how to do this, check the archives. - Original Message From: OZGE ENGIN <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Friday, August 24, 2007 10:45:14 AM Subject: [gmx-users] Unusual structures generated by GENCONF command and resultant minimization problem Hi gromacs-users, I want to simulate a box of that is composed of capped (ACE and NME to N and C termini, respectively) tryptophan molecules. As a first stage, I minimized single capped trp molecule, and then used it with genconf command along with the options -rot ans -nbox. In this case, I changed the gro file of capped trp molecule such that it was treated as a single molecule rather than three (cappes and the trp molecule itself). (It was necessary to be able to use that molecule with genconf command.) After that, I could obtain a box of trp molecules. However, when I looked at it by using VMD, I saw that some of them had unusual bonds. So it caused not to minimization of my system. The steepest descent minimization was terminated before the desired criterion was reached. Although I used a minimized capped trp molecule with genconf command, the resultant box contained some trp molecules that have unusual structures. How can I overcome that problem? Thanks in advance... Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Got a little couch potato? Check out fun summer activities for kids. http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The energy minimization....
The end structure is the same as the start because gromacs cannot find a lower energy structure than the initial one. This indicates something severely wrong, either with the topology or starting structure. You could get a better idea of what's going on by telling gromacs to output structures every step in the minimisation, and examining these so you can actually observe what is happening to your ATP. I've occasionally seen similar results from minimisation, but only after doing something REALLY bad, like precisely overlaying two molecules on the same coordinates. Debugging something like this is probably something only you are going to be able to do, as there are just so many potential ways a suitably, uh, imaginative user can mess things up. - Original Message From: MoJie Duan <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Friday, August 17, 2007 11:15:40 AM Subject: Re: [gmx-users] The energy minimization Hi, Mark: I have done the energy minimization and simulation of ATP in vacuum individual ( Maybe you have suggested me to do this yesterday, but actually I did not understand it, and just do this in solution). There are following problems: 1. in the energy minimization, the potential energy is positive and in 14th step, it's potential energy is "nan". But the ".gro" outfile of "mdrun" is just the same as the original file (i.e. the .gro file before minimization), the return messages of mdrun is (there are not any warning): -- Getting Loaded... Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1# Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps= & #160;200 Step=0, Dmax= 1.0e-02 nm, Epot= 1.06678e+05 Fmax= 3.63368e+06, atom= 26 Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 3.63313e+06, ^^^ atom= 26 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1. Potential Energy = 1.0667836e+05 Maximum for ce = 3.6336775e+06 on atom 26 Norm of force =nan ___ 2. in the full MD simulation, the "warning" coming, the messages is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.881911 (between atoms 27 and 28) rms nan bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 27 28 90.00.1610 0.3030 0.1610 Wrote pdb files with previous and current coordinates step 2490, remaining runtime: 0 s & #160; Writing final coordinates. Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1# step 2500, remaining runtime: 0 s __ And in the ".gro" file after this step, the coordinates of all atoms are "nan". So it means there are crash in the structure? Is the crash between the atom 27 and 28? How to modify the structure file make it normal? Thank you very much! Duan >MoJie Duan wrote: > > >So look at your structures like I said last time! I'm not her e to give > > >my valuable time giving free advice in order to have it ignored... > > Thank you very much for your kindness and patience. Maybe sometimes my > > questions seems to be silly and boring, my knowledge about GROMACS is > >really lack, sorry. > > >Actually, I really cannot understand what you said yesterday. Did you > >mean is there any difference between the atom coordinates of ATP before- > >and after- minimization? > There would normally be some differences visible. If your topology was > badly broken, then you would usually see where it was broken. > >I found there are not any difference between > >these two structure. > >(There are also not any obvious collision between atoms of ATP when > >represent it by Rasmol) > OK, so that means your structure is in a flat area of the potential > surface defined by your topology. If the topology is sound, then you're > in business. > My first recommendation was to minimize and/or equilibrate these > structures on their own, and now I suggest doing them also in solvent. > This will help you eliminate sources of problems and guide you to > what the real problem is. Divide and conquer... > That's fine, then. > OK, so here's your problem. Work out what's breaking and why. Read the > error messages and look at the structures. Understand what each of > your > .mdp file optio
Re: [gmx-users] energy minimization using double precision gromacs failed
There's probably a problem either with your structure or your topology. Spend some time looking at what you've done. I'd start by investigating atom 483. It should be pretty obvious what's wrong, with a force like that. - Original Message From: Q733 <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, August 13, 2007 10:08:34 AM Subject: [gmx-users] energy minimization using double precision gromacs failed Hello, gmx-users,I tried to energy minimize a lipidbilayer consisting of 32 lipids(16 up and 16 down) with two water layers(428 up and 428 down). my em.mdp is like this: title= cpp = /lib/cpp include = define = -DFLEXIBLE constraints = none ;h-bonds lincs_iter = 4 ; RUN CONTROL PARAMETERS = integrator = l-bfgs tinit= 0 dt = 0.2; ps nsteps = 6000 nstxtcout= 100 ; pos to xtc file nstlist= 5 ns_type= grid rlist= 0.7 coulombtype= PME rcoulomb= 0.7 vdw-type= Cut-off rvdw= 0.7 fourierspacing= 0.095; default to 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes ; ENERGY MINIMIZATION OPTIONS = emtol= 0.1; default to 100 emstep= 0.5; default to 0.01 nstcgsteep= 1000 The em is done using double-precision gromacs program,and the out put is like this: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1e-05 writing lowest energy coordinates. Low-Memory BFGS Minimizer converged to machine precision in 7 steps, but did not reach the requested Fmax < 1e-05. Potential Energy = 1.25811048952284e+15 Maximum force = 5.23956606456297e+17 on atom 483 Norm of force = 6.77707038974525e+15 How can I prevent it from converging to machine precision? Is there any method to change the standard of machine precision? Any suggestion will be appreciated , thanks a lot. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Storage of large output files
I've always used HDDs for the main backup/working copies, and DVDs for longer-term backup. You can get hold of 100x spindles of DVDs quite cheaply these days... I wouldn't call it convenient, though. - Original Message From: Monika Sharma <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, August 9, 2007 10:48:52 AM Subject: Re: [gmx-users] Storage of large output files Thanks Mark for your reply. Thats a sound advice. I will really take care of. Actually, through my previous mail, I wanted to know that what other groups are using as storage devices for the backup of their large files, that must have figured out that which way is best-" economical and efficient" way to store their data. Regards, Monika Mark Abraham wrote: > Monika Sharma wrote: >> Dear All, >> We have started our venture into MD recently, for which we are using >> our in-house resources. Now that MD runs are giving very large output >> files like for trr files. The files keep piling up and using spaces >> on the work machines. This is creating problems with the depletion of >> space with every run. Can anyone please suggest an "economical and >> efficient" way how to take backup of such a large files of the order >> of Gb or so, so that we dont end up piling up our work machines with >> such files. And the data need to be saved for future references.. > > First, consider whether you are producing more output than you need. > Look at the options for output frequency of positions and velocities > in .trr files, whether you should be using .xtc files, and whether you > should only be outputting subsets of your data. > > Normally you only want a full frame of positions and velocities in > your .trr file with frequency with which you might ever want to do an > exact restart (and make sure your energy output frequency is a > suitable multiple so you also have energies at this time). This > frequency is invariably much smaller than the frequency with which you > want output data. If you only want position data for your solute for > your later analysis, then outputting only that group to an .xtc file > with frequency as low as you'd ever need will be a tiny fraction of > the cost of a .trr file of the whole system with positions and > velocities at every step. Be aware that analysis types that require > autocorrelation functions need data sampled much more frequently than > the characteristic times of the system. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding total time elapsed
tpbconv -extend ??? - Original Message From: gurpreet singh <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Wednesday, July 25, 2007 6:21:06 PM Subject: [gmx-users] problem regarding total time elapsed Hello users I am using gromacs 3.3 with 43a1 force field. My question is that if i run a simulation say for 50ns , Then if i carried out another md after this one than its time should start from ahead of 50 and not again from the beginning. but in my case everytime the time starts from the beginning. I know its a very basic question which i should not ask from the intelligentsia but this is irritating me from quiet a long time. so please tell me if this is a usual behaviour or some mistake is there in the input file input file : title= third at contant pressure equilibration integrator = md dt = 0.002 nsteps = 25000 nstxout = 500 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = cut-off Tcoupl = berendsen pcoupl = berendsen tau_t= 0.1 0.1 0.1 tc_grps = protein SOLCL- ref_t= 300 300 300 ref_p= 1 1 1 tau_p= 1 1 1 compressibility = 4.5e-5 4.5e-5 4.5e-5 pcoupltype = isotropic define = -DPOSRES comm_mode= angular constraints = hbonds constraint_algorithm = shake gen_vel = yes gen_temp = 300 After every run i am using the output gro file as an input for the next run Thanks & Regards Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restarting a run using tpbconv
I noticed the time provided was: tpbconv -s protein.tpr -f protein.trr -o protein2.tpr -time -1300 I'd have thought Gromacs would have provided an error if this were the case, but it may be that it's taken the frame closest to the (negative) time requested, and consequently just removing the minus sign would fix it? - Original Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Sunday, July 22, 2007 3:00:06 AM Subject: Re: [gmx-users] restarting a run using tpbconv Yang Ye wrote: > The velocity is in the trr file. How many frames you have in > protein.trr? What's its last frame? > You also need to supply the energy file to tpbconv. For an exact restart you need a frame with positions, velocities, and for (e.g.) pressure coupling, an energy file. See section 7.3 for the .mdp options that control how often these get output. You're stuck with whatever problem your previous choices have created, however. The energy file will not create velocities... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
Fair enough, but I'll just repeat that g_bundle does *exactly* what you want in your example - provide it with an index file with two groups with the COMs defining the ends of the axes (in your case, one C in one group and one O in the other) and the option -z, and it'll dump out a file of the angle those axes make with the z-axis. Don't be put off by the way it appears to be designed for helices. - Original Message From: Arneh Babakhani <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, July 17, 2007 1:30:22 AM Subject: Re: [gmx-users] which tool to use a measure a user-defined angle in a traj ok, thanks. I like Chris's suggestion. I'll try using matlab to parse it out (b/c matlab can easily ingest column formatted data), Arneh Tsjerk Wassenaar wrote: > Hi Arneh, > > I think you're out of luck here. However, this is an excellent > exercise to get started with writing custom made analysis tools :) > Alternatively, you could output the coordinates for the C and O using > g_traj and use a script to calculate the angles with the z-axis, in > case it's a single bond you're interested in. > > Cheers, > > Tsjerk > > On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: >> Hi, >> >> Looking through the gmx tools . . . was wondering, which tool would one >> use (if such a tool exists) to measure the fluctuation of a user-defined >> angle in a trajectory. >> >> For instance, I want to measure the angle defined by a carbonyl vector >> (a vector going through a C=O bond) in my molecule and the z-axis of the >> simulation box. How do I define this angle, and which tool would I use >> to measure it in each frame of my trr? >> >> Thanks, >> >> Arneh >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Shape Yahoo! in your own image. Join our Network Research Panel today! http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to simulate peptide capped with ACE?
For some reason this didn't send to the mailing list... I use C-terminal amidated peptides, which sounds similar to what you're trying to achieve. Still, more info about what you've done would have made this reply rather shorter. Is the residue still there after pdb2gmx, for instance? I've never seen grompp remove residues, normally, it exits if something is wrong. What I do is: I have a residue in my .rtp for the amino group, and specify the amide as a seperate residue in . When running pdb2gmx, I select the "none" option for that terminus. This works well for me, never seen a problem. Perhaps the format of your ACE entry in your .rtp isn't appropriate... if you're using the preexisting entry, it won't work because there isn't a bond designated to connect it to the backbone (I think). For instance, I have the line: -C N in my [ bonds ] section - check the 3.3 manual, section 5.5.1. - Original Message From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, July 11, 2007 2:41:17 PM Subject: [gmx-users] How to simulate peptide capped with ACE? Hi, Mark Thank you for your reply. I¡¯m sorry that I didn¡¯t say my question in detail. I want to simulate the peptide capped with ACE group. I use the ffG43a1 force field. I read some suggestions in mailing list archive and named the residue in the initial structure. I used pdb2gmx and it works well. But when I run grompp, I got the warning ¡± No default G96Angle types, using zeroes.¡±. I check the structure and found that the ACE group disappears. Can you tell me why or how to correct it? Thank you very much! fufeng Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] obtaining information from trj file
Check out the file template.c, in gromacs/share/template. I'm being rather rude, and assuming you haven't read the FAQ, of course. - Original Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, June 21, 2007 2:16:05 PM Subject: Re: [gmx-users] obtaining information from trj file Dave Segala wrote: > Dear All, > > I have complete my MD run and have produced a .trj file which you know > contains all atom x, v and f for each time step. I know that I can view > this file using gmxdump. Is there a way to actaully get these values using > matlab, C, C++, or even excel to use them? No these are proprietary and protected by DRM. Only GROMACS tools can get the values :-P Redirecting the output gmxdump to a text file and slurping that up is the easiest way, although probably the least elegant. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_bundle!
I've used g_bundle a lot for just this sort of thing. You need to define the top and bottom of the helix as seperate groups, and define them *very* carefully - it does make a difference how you do it, presumably because g_bundle just plots the axis between the COM of both groups? I usually define as close to 1 complete turn of the backbone of the helix at each end as possible. Your output is not surprising, given what you've asked the program for - the axis between two points that precisely overlap ;-) - Original Message From: priyanka srivastava <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, June 20, 2007 3:27:42 PM Subject: [gmx-users] g_bundle! Dear All, I want to calculate tilt angle of a peptide inserted inside the lipid bilayer (i.e. angle between the helical axis and bilayer normal). From previous posts I got an idea that g_bundle wud solve my problem. I am issuing the following on the command line: g_bundle -f test.xtc -s test.tpr -na 2 -z -tu ps This asks me to "Select a group of top and a group of bottom atoms" Group 0 ( System) has 12877 elements Group 1 ( Protein) has 102 elements Group 2 ( Protein-H) has79 elements Group 3 ( C-alpha) has10 elements Group 4 (Backbone) has31 elements Group 5 ( MainChain) has41 elements Group 6 (MainChain+Cb) has49 elements Group 7 ( MainChain+H) has54 elements Group 8 ( SideChain) has48 elements Group 9 ( SideChain-H) has38 elements Group10 ( Prot-Masses) has 102 elements when I chose "1" and "1" it gives all angles as 90, which is wrong and bun_tiltr is reported as "nan". The manual says that "the program reads two index groups and divides both of them in -na parts". I am a lil confused! what should be my choice here? regards, Pri... Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. http://tv.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tpbconv restart crashing on 3.3.1
yes, tpbconv has been given the energy file. gmxcheck says trr and edr files look happy, the original .tpr looks fine from gmxdump and doesn't crash when it's rerun, and any output from tpbconv looks fine from scanning bits of it in text format, though it's a pretty massive file and I've no idea what I'm looking for. Any suggestions as to keywords to run searches for in these files? I've tried various permutations of warning, error, etc. - Original Message From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Sunday, June 10, 2007 4:15:29 PM Subject: Re: [gmx-users] tpbconv restart crashing on 3.3.1 Alan Dodd wrote: > Hello all, > A recent simulation has been running on a cluster for a couple of weeks. > 5.something-ns in it crashed due to a hardware glitch. All perfectly > understandable so far. > The strange thing is, using tpbconv now results in a .tpr that crashes in the > first step due to massive LINCS errors. Even if you use the option -time to > take the simulation way back, to say 0.5ns when it ought to still be fine, it > still crashes. Other simulations on the same hardware+software are running > fine, other restarts from other jobs crashing at the same time have worked > fine, so it doesn't look like a bug. Any suggestions as to why LINCS errors > could suddenly now prevent the simulation from running *any* of the steps > that it previously ran just fine? I just want a hint as to what we could > have missed, really. > > Alan Dodd > UoB Did you give tpbconv the energy file as well? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Coordinate file does not match topology
Small errors like that are usually down to things like running genion and not changing the .top. I think I made a problem for myself once with non-consecutive atom numbering, too. - Original Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Friday, June 8, 2007 3:48:28 AM Subject: Re: [gmx-users] Coordinate file does not match topology Sheyore Omovie wrote: > Dear gromacs users, > While trying to preprocess my files with grompp, i got the ff error > message: > "Number of coordinates in coordinate file (b4em.gro, 2312) does not > match topology (twopolypeptide.top, 2291)" > How can I fix this? Make them match. Assuming you haven't managed a gross mismatch of files, your [molecules] section of your .top probably isn't right. Chapter five of the manual is your friend here. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php The fish are biting. Get more visitors on your site using Yahoo! Search Marketing. http://searchmarketing.yahoo.com/arp/sponsoredsearch_v2.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] tpbconv restart crashing on 3.3.1
Hello all, A recent simulation has been running on a cluster for a couple of weeks. 5.something-ns in it crashed due to a hardware glitch. All perfectly understandable so far. The strange thing is, using tpbconv now results in a .tpr that crashes in the first step due to massive LINCS errors. Even if you use the option -time to take the simulation way back, to say 0.5ns when it ought to still be fine, it still crashes. Other simulations on the same hardware+software are running fine, other restarts from other jobs crashing at the same time have worked fine, so it doesn't look like a bug. Any suggestions as to why LINCS errors could suddenly now prevent the simulation from running *any* of the steps that it previously ran just fine? I just want a hint as to what we could have missed, really. Alan Dodd UoB The fish are biting. Get more visitors on your site using Yahoo! Search Marketing. http://searchmarketing.yahoo.com/arp/sponsoredsearch_v2.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Regarding membrane protein solvation
Check the manual for 'genbox'. Once you work out how to use it, remember to check your output for waters within the bilayer - I'm not sure how big the cavities are, but I wouldn't be surprised if you could fit a water molecule or two in. - Original Message From: naga raju <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Friday, June 1, 2007 8:07:08 AM Subject: [gmx-users] Regarding membrane protein solvation Dear gmx users, I inserted mebrane protein in DOPC lipid bilayer, some part of protein is outside of lipid bilayer. Would you tell me how to add water molecules to protein(to the out side of lipid bilayer part) around 6 angstroms radius. any suggestion is appreciated. with best regards, Nagaraja. Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] calculation of distance , angle ,dihedral
Read the manual. There's a section on available analysis programs towards the back, all of which start with g_ If I were you, I'd narrow my search to something along the lines of: g_dist, g_angle, and g_dihedral. That might be uncannily helpful. - Original Message From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, May 28, 2007 1:57:45 PM Subject: Re: [gmx-users] calculation of distance , angle ,dihedral [EMAIL PROTECTED] wrote: > HI > > Everybody, thank you for check my mail. > > I am new one on Gromacs, Now I have three problems ,I need to do some > calculation ,please help me ! Thank you! > > 1. the distance of two specified atoms . > > 2. angle of three specified atoms. > > 3.dihedral of four specified atoms > > If commands, in detail the better! I don't know the context in which you want to do these measurements, and I can't read minds. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. http://tv.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Trjconv: reducing frames and Time issue
Don't use -timestep. Just -skip will do for what you want. - Original Message From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, May 8, 2007 7:20:39 PM Subject: [gmx-users] Trjconv: reducing frames and Time issue Hello All, I have a xtc file and I used trjconv on it to reduce the number of frames using: trjconv -f original.xtc -o reduced-frames.xtc -s xx.tpr -timestep 20 -fit rot+trans -skip 2 -center no Now I have two xtc files for a 10ns simulation: original.xtc reduced-frames.xtc I did gmxcheck to check the number of frames and time (I will show the results for both below). The problem is: the number of frames is reduced by half however the time shown on the reducedframes.xtc is increased!! (from 10 000 ps to 100 000 ps).. I cant understand what this means? I did a g-cluster analysis and they r saying I did a 100 000ps simulation which it not true! can anyone explain this to me? original.xtc Reading frame 0 time0.000 # Atoms 5100 Precision 0.001 (nm) Last frame 5000 time 1.000 Item#frames Timestep (ps) Step 50012 Time 50012 Lambda 0 Coords50012 Velocities 0 Forces 0 Box 50012 reduced-frames.xtc Reading frame 0 time0.000 # Atoms 92 Precision 0.001 (nm) Last frame 2500 time 10.000 Item#frames Timestep (ps) Step 250140 Time 250140 Lambda 0 Coords250140 Velocities 0 Forces 0 Box 250140 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ED analysis: help on cosine content and overlap of the fluctuations
Short answer? RMSD is a lousy measure of convergence :) - Original Message From: Caterina Arcangeli <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[EMAIL PROTECTED]> Sent: Friday, April 13, 2007 10:58:54 AM Subject: [gmx-users] ED analysis: help on cosine content and overlap of the fluctuations Dear all, I performed essential dynamics (ED) analysis on my protein (253 amino acids). The simulation (10ns) achieves stability in the RMSD after 6.0ns, but a convergence analysis based on cluster analysis (as described by Daura, 1999) indicates that the conformational sampling reaches a stable value only for the last 1.0ns. So, I've performed ED on both 6-10 ns (M1) and 9-10ns (M2) time interval using g_covar. To check if the principal modes are well defined, I've calulated the ovelap of the sampling between the first and second half of the trajectories (I've splitted M1 and M2 into two halves) and the cosine content of the first eigenvectors: - the normalized overlaps are 0.499 (M1) and 0.434 (M2); - the subspace overlaps (rmsip) for the first 10 eigenvectors are 0.748 (M1) and 0.686 (M2); - the cosine content of the first eigenvectors is 0.828 (pc1) for M1 and 0.125 (pc1) for M2. So, apparently, the two method are inconsistent: a higher rmsip value is observed for M1 (according to Amadei, a rmsip value > 0.7 shows a reasonable convergence) wheras the lower cosine content is obtained for M2 (according to Hess, a value < 0.5 indicates jumping between clusters and not a merely random diffusion). My questions are: which time window better describe the dynamics of my protein? From where come out this inconsistency? What I'm wrong? Thank to all. Caterina P.S. I aware that 10 ns are in general insufficient to describe the thermodynamics of a protein but I want just to have an idea of some structural properties of my protein. ___ gmx-users mailing list[EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing list[EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restarting a sorted shuffled trajectory
>From memory, deshuffling, followed by using editconf to change confout.gro to >a pdb and back again, results in the molecule types all being in the same >order again (in my case, protein, lipid, solvent, ions instead of protein, >lipid, ions, water, lipid, ions, water, lipid, ions, water, protein etc). >Actually... I think ions might move about, but this process at leasts put them >all in the same place, even if you then have to check which order the groups >are in. I couldn't say for certain if the molecules within a set group stay >in the same order, but this can at least let you use the same .top with >minimal or no alterations. - Original Message From: Stéphane Téletchéa <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, February 12, 2007 5:00:24 PM Subject: [gmx-users] restarting a sorted shuffled trajectory Dear all, I'm willing to do a fine-tuning start for my simulation using multiples prX.mdp input. I'm launching the first run using -shuffle -sort from grompp (with pr1.mdp), but i'd like to know how to reuse the resulting .trr file for the second pr (pr2.mdp). I've tried deshuffling first the trr file but do i also need to desort it ? (as Chris Neale posted on 24.01.2007 on this list) So far, i'm getting: Warning: atom names in ../test_min_deflated26_sol_ions.top and ../toto_min_formd.gro don't match (HW2 - HW1) (more than 20 non-matching atom names) WARNING 1 [file "../test_min_deflated26_sol_ions.top", line 38]: 23642 non-matching atom names atom names from ../test_min_deflated26_sol_ions.top will be used atom names from ../OR1G1_min_formd.gro will be ignored The mdrun was launched after this grompp input : grompp_lam \ -f mdp/md_Na.mdp \ -p test_min_deflated26_sol_ions.top \ -pp test_min_deflated26_sol_ions_out.top \ -c toto_min_formd.gro \ -o fullmd_ions.tpr \ -po md_Na_out.mdp \ -deshuf fullmd_ions.ndx \ -shuffle \ -sort \ -np 4 I'd like to pursue the dynamics, so far i'm doing: cd test grompp_lam \ -f ../mdp/pr1.mdp \ -p ../test_min_deflated26_sol_ions.top \ -pp test_out.top \ -c ../toto_min_formd.gro \ -t ../fullmd_ions_deshuf.trr \ -e ../fullmd_ions.edr \ -n toto_min_formd.ndx \ -o test.tpr \ -po test_out.mdp \ -np 4 Thanks a lot for your comments/advices. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] eneconv error
I've noticed something similar... it's worth noting that you appear to be getting duplicates around the join mark. I suspect, for me at least, it's because my .edr output interval doesn't quite tally with the total runtime - so I not only get a output at every required step, but also a final output at a non-specified interval, still included in the fixed.edr but ignored usually - providing your extra 4 frames. Or it could be an extra frame at the start, of course. - Original Message From: chetana baliga <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, January 30, 2007 2:35:46 PM Subject: [gmx-users] eneconv error Dear users, I am getting extra frames upon concatenating my edr files. I am using a time step of 0.5 ps . Each edr file , of 2 ns, has exactly 4000 frames, but upon concatenating files of total of 10 ns, I am getting 20004 frames. But, my xtc files upon concatenation give me the required number of frames !! [i.e., 2 in this case!] I am unable to figure out how this could be occuring. Thanks for any help in advance :) Regards, Chetana. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem running posre
Have you tried running for a short period without PR, then putting the output from that into PR again? If the initial run is short enough, it shouldn't affect things too much, but may still randomise out whatever's causing the problem. - Original Message From: andrea spitaleri <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, January 30, 2007 2:10:33 PM Subject: [gmx-users] problem running posre Hi all, I am encountering in a very strange problem. Feeding a protein (after minimization) to a position restraints simulation after few steps (10-20) I am getting this crash error: "Number of grid cells is zero. Probably the system and box collapsed" However, submitting with the same input a simulation with "no" position restraints the runs goes fine. I tried using posrefc 1000 and lower (200). Same result. Any suggestion? Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=list&sid=396546091 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: long range energy
Incidentally, if PME has been specified correctly, am I right in assuming there should be an energy term available within g_energy for long range forces? Which one is it? For some reason, I haven't been able to find it yet. - Original Message From: Richard Vadnais <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, January 22, 2007 1:46:52 PM Subject: [gmx-users] Re: long range energy > Richard Vadnais wrote: >> hi all, >> >> I want to find four types of energies from my simulation: LJ and >> Coulomb at long and short range. I use PME for coulomb type and cut-off >> for VdW type with rlist = rcoulomb = 0.9 >> >>However, the LJ (LR) and Coulomb LR are not generated in the output >> nor can I get them with g_energy. > > That's because they aren't defined when rlist = rcoulomb. Have a read of > the relevant manual sections. > > Mark > > I read these sections and this is where I am confused. It is specified that PME cannot be used with rlilst different than rcoulomb but that if they are egal, long range energies would not be defined. However, I am trying to reproduce a simulation done by a former member of our research group and from the input files (.mdp) he used, I found that he used: rlist = 1.05 rcoulomb 1.15 coulombtype = PME From what I gathered from the manual, this combinaison is not possible, however, not only did he get results from this input, but he had the four types of energies: LJ-(SR), LJ-(LR), coulomb-(SR), coulomb-(LR). (I should have been more precise in my first post. I apologies.) thanks for your help, Richard Vadnais, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] inconsistent XTC/Magic number error in g_density
Have tested the problem some more - and submitted a bugzilla - problem appears to be a generic issue with skipping chunks of trajectory larger than 2.something GB (looks like the size of an int). - Original Message From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Wednesday, January 17, 2007 8:10:22 PM Subject: Re: [gmx-users] inconsistent XTC/Magic number error in g_density Alan Dodd wrote: > g_density produces an error every time I try to run it on two of my > trajectories at frame 0 - magic number for one, and a ridiculous number of > atoms for the other. Oddly, every other program I've used (trjcat, trjconv, > g_covar, g_dist, etc etc) is perfectly happy with the files, and gmxcheck > also produces a happy-looking output. Any clues what the problem could be? > You'd think as it uses the same code (xtcio.c) for reading xtc's for all > analysis, they'd all either succeed or fail... > > g_density: > Reading frame 0 time0.000 > --- > Program g_density, VERSION 3.3.1 > Source code file: xtcio.c, line: 233 > Fatal error: > Frame contains more atoms (1865562167) than expected (42549) > > gmxcheck: > Checking file trjcatted.xtc > Reading frame 0 time0.000 > # Atoms 42575 > Precision 0.001 (nm) > Last frame 6 time 45000.000 > > Item#frames Timestep (ps) > Step 600010.75 > Time 600010.75 > Lambda 0 > Coords 600010.75 > Velocities 0 > Forces 0 > Box 600010.75 > Is your g_density from the same build as the other programs? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] inconsistent XTC/Magic number error in g_density
yes, all programs are from the only build of gromacs on that machine. I've subsequently installed a local version of 3.2.1 to try that, the g_density from it works fine. So I guess maybe it's not the xtc after all? - Original Message From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Wednesday, January 17, 2007 8:10:22 PM Subject: Re: [gmx-users] inconsistent XTC/Magic number error in g_density Alan Dodd wrote: > g_density produces an error every time I try to run it on two of my > trajectories at frame 0 - magic number for one, and a ridiculous number of > atoms for the other. Oddly, every other program I've used (trjcat, trjconv, > g_covar, g_dist, etc etc) is perfectly happy with the files, and gmxcheck > also produces a happy-looking output. Any clues what the problem could be? > You'd think as it uses the same code (xtcio.c) for reading xtc's for all > analysis, they'd all either succeed or fail... > > g_density: > Reading frame 0 time0.000 > --- > Program g_density, VERSION 3.3.1 > Source code file: xtcio.c, line: 233 > Fatal error: > Frame contains more atoms (1865562167) than expected (42549) > > gmxcheck: > Checking file trjcatted.xtc > Reading frame 0 time0.000 > # Atoms 42575 > Precision 0.001 (nm) > Last frame 6 time 45000.000 > > Item#frames Timestep (ps) > Step 600010.75 > Time 600010.75 > Lambda 0 > Coords 600010.75 > Velocities 0 > Forces 0 > Box 600010.75 > Is your g_density from the same build as the other programs? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] inconsistent XTC/Magic number error in g_density
g_density produces an error every time I try to run it on two of my trajectories at frame 0 - magic number for one, and a ridiculous number of atoms for the other. Oddly, every other program I've used (trjcat, trjconv, g_covar, g_dist, etc etc) is perfectly happy with the files, and gmxcheck also produces a happy-looking output. Any clues what the problem could be? You'd think as it uses the same code (xtcio.c) for reading xtc's for all analysis, they'd all either succeed or fail... g_density: Reading frame 0 time0.000 --- Program g_density, VERSION 3.3.1 Source code file: xtcio.c, line: 233 Fatal error: Frame contains more atoms (1865562167) than expected (42549) gmxcheck: Checking file trjcatted.xtc Reading frame 0 time0.000 # Atoms 42575 Precision 0.001 (nm) Last frame 6 time 45000.000 Item#frames Timestep (ps) Step 600010.75 Time 600010.75 Lambda 0 Coords 600010.75 Velocities 0 Forces 0 Box 600010.75 --- g_density: Reading frame 0 time0.000 --- Program g_density, VERSION 3.3.1 Source code file: xtcio.c, line: 83 Fatal error: Magic Number Error in XTC file (read -121802304, should be 1995) gmxcheck: Note: tpx file_version 31, software version 40 Checking file trjcatted.xtc Reading frame 0 time0.000 # Atoms 42449 Precision 0.001 (nm) Last frame 6 time 45000.000 Item#frames Timestep (ps) Step 600010.75 Time 600010.75 Lambda 0 Coords 600010.75 Velocities 0 Forces 0 Box 600010.75 Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] box size for simulation of membrane protein
Original Message From: Mohamed Osman <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Thursday, January 11, 2007 10:49:29 PM Subject: [gmx-users] box size for simulation of membrane protein My questions: 1. Protein is closer to one edge than the other. Does this make any difference? The solvants are part of equilibritaed lipid. -Shouldn't do. It's still the same distance from its periodic image on each side, which is what matters. As long as it's in the correct place in the bilayer, I don't believe there are any 'edge effects' in the implementation of PBC in gromacs you need to worry about. Along protein axis: a. The periodic image is 1.43 nm away. (along protein axis) b. The distance between the protein and its mirror image is: 0.8 nm on one side and 2.0 nm on the other side? (These affect PME - coulmb interactions). Will these cause trouble? -The minimum protein-image distance is all that matters. It doesn't matter how close the protein is to one side of the box - if it's closer on one side, it's further on the other. Unless you mean different distances on the x and y axis? -As far as I know, PME sums out to infinity, so you can't really change that. BUT: 2. Is it necessary to keep the protein at least 1.5 nm away from the edges normal to z-axis? This more than doubles the number of solvant molecules. I have simulations with less than 50,000 atoms (protein, solvants, and KcsA). But no one realy says much about the box sizes. What is the common practice? Please give examples? and How much compromise is acceptable ? -The official requirement is for the minimim distance from protein to its periodic image to be double the cutoff, so that no atom feels forces from more than one image of the protein. However, you can probably get away with reducing that minimum distance to slightly more than the cutoff (1.5nm in your case) which just stops the protein from interacting with its own periodic images. Most people work on this basis, on the grounds it probably doesn't matter if the water molecules are 'feeling' more than one protein. It's a judgement call really, depending on how badly you want it to run faster vs how much you lose by making it do that. "It is common to compormize in this respect !!!" Thanks Mohamed Osman === Professor of Electrical Engineering Washington State University Pullman, WA 99164-2752 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to calculate the area of per lipid in membrane
I don't know of anything publicly available, but have a look around for voronoi cell analysis. People have used it before for lipid area calculation, and may be willing to let you use their code. Alternatively, read up on the theory and try it yourself. - Original Message From: linfu <[EMAIL PROTECTED]> To: gmx-users Sent: Wednesday, December 20, 2006 9:14:26 AM Subject: [gmx-users] how to calculate the area of per lipid in membrane Dear gmx community! Could anyone help me how to perform the analysis of after MEMBRANE simulation in NPT condition. because there is a protein inserted in the membrane, it is difficult for me to calculate the area of per lipid directly. what kinds of program can do such work. Thank you very much in advance! BEST REGARDS Fu Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS exit codes; error in LAM installation?
Hello, (background) I recently compiled a new version of the 3.2.1 mdrun to make use of the lam 7.1.2 that's just been installed. For some reason, I can't get a run to work with it - it goes fine until: Back Off! I just backed up enerG.edr to ./#enerG.edr.1# starting mdrun '?' 143 steps, 2145.0 ps. whereupon one of the processes (always n3, no matter which physical machine it is) exits for no obvious reason. The signal given is 11 - I can't find reference to this in the Gromacs or lam source, so I don't know what it means. Cranking up the verbosity on everything I can sheds no further light on it. I'm guessing I did something not quite right in the installation, but without more information, there's no way to know how to fix it. Anyway: So, does anyone know what this exit code means? (and, ideally, how to avoid it...) Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Creation of an index file with seperate lipid leaflets
Thanks to all for your help/suggestions. I gave up on modifying make_ndx, the code is just too impenetrable for a weekend scripter like me... Have made a perl script to produce a .ndx file with 2 groups, one containing all upper leaflet atoms, the other lower. --- Patrick Fuchs <[EMAIL PROTECTED]> wrote: > Hi, > I've written a python script that does what you > want. > I cleaned the script (make_2leaflets_index) and put > it on my web page at > the following URL: > http://condor.ebgm.jussieu.fr/~fuchs/download/index.html > Hope it helps. > Ciao, > > Patrick > > Jay Mashl a écrit : > > Wasted work would be bad ;) > > > > Rather than headgroup orientation, maybe try > looking at atom distributions > > along the bilayer normal direction. Neutron > scattering experiments show that > > for atom groups far from the bilayer midplane, the > corresponding z-coordinates > > form two distinct distributions. So one way could > be the following. Pick a > > headgroup atom and obtain its z-coordinate. Have > make_ndx accept this value as > > input. Search the system by looping over lipids > and ask whether that atom type > > has a z-coordinate within some amount around the > input value. From this you > > know the membership of the leaflets. A more > automatic way would be to have the > > program first discern the distribution and then > reread the system to decide the > > leaflet membership. > > > > Jay > > > > > > On Wed, 8 Nov 2006, Alan Dodd wrote: > >> Wouldn't shuffle/sort undo all the good work? I > did > >> wonder if I should have labelled the lipids in > >> different leaflets as different molecule types, > or > >> different chains, but it's a bit late now... > >> > >> --- Jay Mashl <[EMAIL PROTECTED]> wrote: > >> > >>> On Wed, 8 Nov 2006, Alan Dodd wrote: > >>>> Has anyone already created a way to generate an > >>> index > >>>> file with the atoms from the two leaflets of a > >>> bilayer > >>>> listed seperately? I can't believe it hasn't > >>> already > >>>> been done, but can't find a direct description > of > >>> a > >>>> solution. I'm attempting a modification to > >>> make_ndx, > >>>> (or perhaps something considerably less > ambitious, > >>>> judging by the way it's going so far) to permit > >>> lipid > >>>> selection based on headgroup orientation, > though > >>> I'd > >>>> quite like to save myself the effort. > >>>> Incidentally, splitres and splitat seem to be > the > >>>> wrong way around, unless I'm misunderstanding > them > >>> - > >>>> they do the opposite of what they say. From > the > >>>> gromacs 3.3.1 source download I did on April of > >>> this > >>>> year. > >>> Reordering the lipids into leaflets in your > starting > >>> coordinate > >>> file might be a good idea. If you anticipate > lipid > >>> exchange between leaflets, > >>> then a more general tool like what you suggest > would > >>> be helpful. > >>> > >>> Jay > >>> > >>> ___ > >>> gmx-users mailing listgmx-users@gromacs.org > >>> > http://www.gromacs.org/mailman/listinfo/gmx-users > >>> Please don't post (un)subscribe requests to the > >>> list. Use the > >>> www interface or send it to > >>> [EMAIL PROTECTED] > >>> Can't post? Read > >>> http://www.gromacs.org/mailing_lists/users.php > >>> > >> > >> > >> > >> > >> > > >> Sponsored Link > >> > >> Mortgage rates near 39yr lows. $420k for > $1,399/mo. > >> Calculate new payment! > >> http://www.LowerMyBills.com/lre > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please don't post (un)subscribe requests to the > list. Use the > >> www interface or send it to > [EMAIL PROTECTED] > >> Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > >&g
Re: [gmx-users] Creation of an index file with seperate lipid leaflets
Wouldn't shuffle/sort undo all the good work? I did wonder if I should have labelled the lipids in different leaflets as different molecule types, or different chains, but it's a bit late now... --- Jay Mashl <[EMAIL PROTECTED]> wrote: > On Wed, 8 Nov 2006, Alan Dodd wrote: > > Has anyone already created a way to generate an > index > > file with the atoms from the two leaflets of a > bilayer > > listed seperately? I can't believe it hasn't > already > > been done, but can't find a direct description of > a > > solution. I'm attempting a modification to > make_ndx, > > (or perhaps something considerably less ambitious, > > judging by the way it's going so far) to permit > lipid > > selection based on headgroup orientation, though > I'd > > quite like to save myself the effort. > > Incidentally, splitres and splitat seem to be the > > wrong way around, unless I'm misunderstanding them > - > > they do the opposite of what they say. From the > > gromacs 3.3.1 source download I did on April of > this > > year. > > Reordering the lipids into leaflets in your starting > coordinate > file might be a good idea. If you anticipate lipid > exchange between leaflets, > then a more general tool like what you suggest would > be helpful. > > Jay > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > Sponsored Link Mortgage rates near 39yr lows. $420k for $1,399/mo. Calculate new payment! http://www.LowerMyBills.com/lre ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Creation of an index file with seperate lipid leaflets
Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Alan Dodd University of Bristol __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] charged lipids
I've been searching through the Gromacs files, site etc looking to see if anyone has used charged lipids in a simulation and can't find any evidence of this. I don't see any reason why this should be impossible to do, granted there'll need to be a fair few counterions, but I'm not intending to do a pure bilayer, just dope the existing one with a few negative charges. And a high concentration of ions near the membrane is not entirely unrealistic, I believe. So does anyone know of any gromacs stuff using negative lipids, or alternatively a reason why this hasn't been done? Thanks, Alan Dodd University of Bristol __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Lipid Bilayer Simulations
Configuring the .itp files etc initially is a bit tricksy without knowing what you're doing, the short not-very-helpful answer is "read the manual". There's a whole chapter (5?) on forcefield files and their formats. It's entirely possible to set it all up so that pdb2gmx does in fact work, but to do this you need to edit the forcefield files in the main gromacs folder for these things (add your lipid.itp and dppc.itp, add "#include" for each of these to your forcefield of choice). Anyways: I'd guess it was complaining initially because #include files were in the wrong order in your .top, and then subsequently because you removed the reference to lipid.itp (which you need). Unless someone can be of more help, I suggest you just tinker. --- toma0052 <[EMAIL PROTECTED]> wrote: > Hi, > I am new to Gromacs, and I am working with > lipid bilayer simulations. > I am attempting to just run an energy minimization > on a lipid bilayer so I > can get a better feel for the program. I have taken > the files dppc128.pdb, > dppc.itp, lipid.itp and example2.itp from Peter > Tieleman's website. > Because I could not use teh pdb2gmx command, I > started with the editconf > command and then the genbox command, both of which > seemed to run > successfully. Then, I tried to do the preprocessing > with the grompp > command, but I received the error; Fatal Error: > Found a second defaults > directive, file "lipid.itp". When I removed > lipid.itp from the topology > file, I received the error; Fatal Error: Atomtype > 'LC3' not found! As I > said before, I am new to Gromacs, and I am not sure > how to get around this > problem. Do I need to put the dppc.itp and lipid.itp > file together into > one? Any help would be appreciated. > > Thanks, > Mike Tomasini > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] make_hole vs. genconf
> > > I'm also aware of the make_hole tool. My question > here is: Does > > make_hole create a hole of specified dimensions > and orientation, > > according to the solute coordinates? And can you > specify exactly > > where in the membrane you want the whole? > > Make_hole doesn't actually make a hole. You need to > make the > premilinary hole yourself. Not true, I've made a hole using make_hole. Manually removing central lipids, and using make_hole to finess the rim of the hole is probably more computationally efficient, but make_hole is perfectly capable of doing what the name says (and less labor intensive). __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints crashing
Interestingly, merging the peptide chains to one results in PR working fine. Smells like a bug to me... but I guess that's the price of using an old version. --- Steffen Wolf <[EMAIL PROTECTED]> wrote: > Yes, so it looks that minimization ended at a > metastable point, which > was surmounted by a free MD run but kept by the PR > and therefore caused > the system to crash. Which minimization algorithm > did you use? Steep or CG? > > -- > Dipl.-Chem. Steffen Wolf > Department of Biophysics > University of Bochum > ND 04/67 > 44780 Bochum > Germany > Tel: +49 (0)234 32 28363 > Fax: +49 (0)234 32 14626 > E-Mail: [EMAIL PROTECTED] > Web: http://www.bph.rub.de > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints crashing
Interesting idea, but multiple different start points have failed with PR, and succeeded with normal MD. Freeze groups seem to be working OK, so I'm using that for now - after all, it doesn't need to be 'real', I just want to equilibrate the lipid/solvent without moving my carefully-placed peptide. Interestingly, I've had similar problems before, but only when I use multiple peptides. Might try merging the chains and see what that does. I used CG with steep every 50 steps... sounds weird I know, but it's proved pretty reliable. --- Steffen Wolf <[EMAIL PROTECTED]> wrote: > Alan Dodd wrote: > > No, minimisation was without PR. Surely > minimisation > > with PR would *increase* bad contacts, rather than > > removing them? I've tried running for a while > under > > normal MD, successfully and without LINCS errors, > then > > taking the endpoint and running under PR, but it > still > > crashes almost instantaneously, so it's unlikely > to > > just be a matter of energies or bad contacts, I'd > have > > thought? > > > > > Yes, so it looks that minimization ended at a > metastable point, which > was surmounted by a free MD run but kept by the PR > and therefore caused > the system to crash. Which minimization algorithm > did you use? Steep or CG? > > -- > Dipl.-Chem. Steffen Wolf > Department of Biophysics > University of Bochum > ND 04/67 > 44780 Bochum > Germany > Tel: +49 (0)234 32 28363 > Fax: +49 (0)234 32 14626 > E-Mail: [EMAIL PROTECTED] > Web: http://www.bph.rub.de > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints crashing
No, minimisation was without PR. Surely minimisation with PR would *increase* bad contacts, rather than removing them? I've tried running for a while under normal MD, successfully and without LINCS errors, then taking the endpoint and running under PR, but it still crashes almost instantaneously, so it's unlikely to just be a matter of energies or bad contacts, I'd have thought? --- Steffen Wolf <[EMAIL PROTECTED]> wrote: > Hi Alan, > well, no, position restraints (and your definition) > seem to be fine, and > they work well with my protein/membrane system. > Sounds more like your > system is still not well minimized. Using the > freezegroup option is not > such a good way, because it will not work well > together with the > pressure coupling. Did you use the restraints during > minimization as well? > Bye > Steffen > > Alan Dodd wrote: > > Hello, > > I'm trying to run position restraints on multiple > > peptides in a protein/bilayer/water system. MD > > *without* position restraints runs absolutely > fine, > > but as soon as I stick that "define = -DPOSRES" > in, > > some of the molecules explode within a matter of > fs. > > Any idea why this might be? Is MD with position > > restraints considerably less tolerant of bad > > structures, energies etc (although the structure > > minimised absolutely fine-only "wrongness" about > it is > > a big hole)? > > Am using 3.2.1. Will probably try defining the > > protein as a freeze group as a temporary > get-around... > > but it'd be nice to find out what's going on. > > > > > > topol.top: > > ; > > ; File 'topol.top' was generated > > ; By user: ad0303 (1002) > > ; On host: hydra > > ; At date: Wed Aug 9 11:21:57 2006 > > ; > > ; This is your topology file > > ; ? > > ; > > ; Include forcefield parameters > > #include "ffgmx.itp" > > > > ; Include chain topologies > > #include "topol_A.itp" > > #ifdef POSRES > > #include "posre_A.itp" > > #endif > > > > #include "topol_B.itp" > > #ifdef POSRES > > #include "posre_B.itp" > > #endif > > > > #include "topol_C.itp" > > #ifdef POSRES > > #include "posre_C.itp" > > #endif > > > > #include "topol_D.itp" > > #ifdef POSRES > > #include "posre_D.itp" > > #endif > > > > #include "topol_E.itp" > > #ifdef POSRES > > #include "posre_E.itp" > > #endif > > > > #include "dopc.itp" > > > > ; Include water topology > > #include "spc.itp" > > > > #ifdef POSRES_WATER > > ; Position restraint for each water oxygen > > [ position_restraints ] > > ; i funct fcxfcyfcz > >11 1000 1000 1000 > > #endif > > > > ; Include generic topology for ions > > #include "ions.itp" > > > > [ system ] > > ; Name > > ? > > > > [ molecules ] > > ; Compound#mols > > Protein_A 1 > > Protein_B 1 > > Protein_C 1 > > Protein_D 1 > > Protein_E 1 > > DOPC 256 > > SOL 9598 > > Cl 25 > > > > > - > > > > posre_whatever.itp (same for all 5 peptides) > > [ position_restraints ] > > ; atom type fx fy fz > > 1 1 1000 1000 1000 > > 5 1 1000 1000 1000 > > 6 1 1000 1000 1000 > > 7 1 1000 1000 1000 > > 8 1 1000 1000 1000 > > 10 1 1000 1000 1000 > > 11 1 1000 1000 1000 > > 12 1 1000 1000 1000 > > etc... > > > > > > > > > > > __ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailin
[gmx-users] position restraints crashing
Hello, I'm trying to run position restraints on multiple peptides in a protein/bilayer/water system. MD *without* position restraints runs absolutely fine, but as soon as I stick that "define = -DPOSRES" in, some of the molecules explode within a matter of fs. Any idea why this might be? Is MD with position restraints considerably less tolerant of bad structures, energies etc (although the structure minimised absolutely fine-only "wrongness" about it is a big hole)? Am using 3.2.1. Will probably try defining the protein as a freeze group as a temporary get-around... but it'd be nice to find out what's going on. topol.top: ; ; File 'topol.top' was generated ; By user: ad0303 (1002) ; On host: hydra ; At date: Wed Aug 9 11:21:57 2006 ; ; This is your topology file ; ? ; ; Include forcefield parameters #include "ffgmx.itp" ; Include chain topologies #include "topol_A.itp" #ifdef POSRES #include "posre_A.itp" #endif #include "topol_B.itp" #ifdef POSRES #include "posre_B.itp" #endif #include "topol_C.itp" #ifdef POSRES #include "posre_C.itp" #endif #include "topol_D.itp" #ifdef POSRES #include "posre_D.itp" #endif #include "topol_E.itp" #ifdef POSRES #include "posre_E.itp" #endif #include "dopc.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name ? [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 Protein_C 1 Protein_D 1 Protein_E 1 DOPC 256 SOL 9598 Cl 25 - posre_whatever.itp (same for all 5 peptides) [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 10 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 etc... __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Disulphide bonds
I use the option -merge with my SS-linked peptides, and pdb2gmx always asks me if I want to join my cysteines with a bond. If they're internal to the protein, perhaps it's either that they're too far apart, or you need -ignh as otherwise they've got hydrogens on and potentially can't bond. --- Cesar Araujo <[EMAIL PROTECTED]> wrote: > Hi, > > Anybody knows if there is some way to tell pdb2gmx > to recognize automatically S-S bonds and not through > the modification of specbond.dat file and -ss > option??? > > Regards, > César.- > > --- > Cesar Araujo, Lic. of Chemistry > Department of Molecular Endocrynology > Oulu University Hospital > FIN-90029 OYS, FINLAND > > phone: +358 8 3155632 > e-mail: [EMAIL PROTECTED] > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Stepsize too small, or no change in energy
I find getting a system minimised is often quite tricky. There's a variety of things that can be fiddled with, using cg with various intervals between steps of steepest descent, running a few steps of md (say, 10 to 100) after minimisation and then minimising again, randomly perturbing the coordinates of the problem atoms manually in the .gro file and retrying, stuff like that. Make sure there's no obvious bad contacts in the structure first, my personal nemesis seems to be lipid tails stuck through tryptophan rings... --- Pradip Kumar Biswas <[EMAIL PROTECTED]> wrote: > Hi, > > What is your 'emstep' value in your mdp file? Could > you try to rerun > your system with a low emstep; say with emstep = > 0.1 > or else? > > pb. > > > On Jul 18, 2006, at 1:13 AM, Srivastava, Dhiraj > (UMC-Student) wrote: > > > Hi all > > > > when i am trying to minimize my structure, i > am getting > > following error. > > > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1000 > > > > Double precision normally gives you higher > accuracy. > > > > writing lowest energy coordinates. > > > > Back Off! I just backed up prodh_em.trr to > ./#prodh_em.trr.2# > > > > Back Off! I just backed up prodh_wb.pdb to > ./#prodh_wb.pdb.4# > > > > Steepest Descents converged to machine precision > in 45 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = -1.8373166e+06 > > Maximum force = 1.5158329e+04 on atom 519 > > Norm of force = 3.1759754e+04 > > > > > > i have tried the conjugated gradient, constraint > none and also > > included flexible water but still i am getting the > same error. > > > > what should i do to solve this problem? > > > > Thanks in advance for help. > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Pradip K. Biswas, PhD. > Research Associate, Department of Chemistry; > Cleveland State University, Ohio-44115 > Phone: 1-216-875-9723 > http://comppsi.csuohio.edu/groups/people/biswas.html > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
