Re: [gmx-users] Question about DNA simulation
Hi, No there were no dummies, and without changing the masses in the non-bonded parameters file it would give infinite velocities. Regards Maik Goette wrote: Hi I never had to change masses in the nb.itp and I ran lots of simulations with the amber-Port...Are you sure, that you had no dummies with mass zero or so? REgards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ George Abadir wrote: Hi, Actually I think that although the .atp file seems to be used, the masses in the ffamberxxnb.itp file must be changed from the zero values to the correct ones: when I ran a simulation without changing them I got infinite velocities and which did nor happen when I changed the masses to the correct ones. Thanks, George David van der Spoel wrote: Maik Goette wrote: David I think, I should not contradict to one of the developers, but if your statement is true: 1. Where, in fact, are the masses coming from (the masses in the amberFF port can only be found in the atp, as far as I know)? 2. Why does GROMACS complain about missing atoms in the atp-file, if I add a new atom type to the nb-section? Just out of curiosity... Hm, no problems contradicting me at least... I presume you're right. ___ 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] conformational distance D4
ravishk kumar wrote: Dear gmx-users, Is it possible to calculate using gromacs, the conformational distance D4 (as given by (Pliska and Marinari, (1993). On heteropolymer dynamics) between all possible pairs of Ca-atoms in a configuration at time t with the corresponding distances in the starting structure ?. Thanks in advance ravishk check g_rmsdist ___ 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. 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 4205 fax: 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
[gmx-users] 2nd Virial coefficient and Hydrophobic moment Calculation
Hi GMX user, Is there anyway I can calculate 2nd virial coefficient and hydrophobic moment using gromacs? I guess 2nd virial coefficient calculated somewhere in the gromacs. Thanking you, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ 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] Basic Query
Hie all, I am currently involved in doing a lipid-peptide simulation under NPAT conditions. The way I have applied NPAT condition is as follows: ref_p = 0 1 compressibility = 0.0 4.5e-5 Although while performing analysis it shows that the x and y dimensions are constant but still I am not sure about the way I have applied NPAT. Could somone please tell me the basis behind it? Another thing is I have used vdwtype: cutoff. But my intention is not to use the twin range cutoff at all!! In my case rlist = rcoulomb = rvdw, i.e. all three are same!! Is this alright? (the coulombtype = PME) waiting eagerly for the reply, Pri... Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222 ___ 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] Inclusion of an angle-angle cross term?
Hi there, I'm working on fitting some force field parameters to a batch of ab-initio single-point force calculations, and the fit still needs improvement. I'm thinking of including an angle-angle cross term in my custom force field, but so far I haven't found that GROMACS can implement this. I think that five atom labels and three parameters are needed to describe such an interaction; can GROMACS do this right now? Thanks. - Lee-Ping Wang ___ 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] website problems
L.S., Just to let you guys know, I'm experiencing some problems with the www.gromacs.org website. E.g.: whenever I press the 'DOCUMENTATION' button on the top menu I get the related page, but not the related submenu on the left side. And whenever I press the 'News' button on the main menu on the left side I get an error: [error] Warning: Invalid argument supplied for foreach() in /data/gmx/www- gmx/administrator/components/com_sef/core/sef.mapper.php on line 431 Warning: Cannot modify header information - headers already sent by (output started at /data/gmx/www- gmx/administrator/components/com_sef/core/sef.mapper.php:431) in /data/gmx/www- gmx/administrator/components/com_sef/core/sef.resolver.php on line 609 The page you are trying to access does not exist. Please select a page from the main menu. [/error] I'm working on a Windows 2000 SP4 machine with IE 6.0 SP1. Emptying the internet cache didn't solve it. Also tried another, similar machine, but same problems. It seems to me the only way of getting to the online manpages for the gromacs utilities now is by using the search-option or via the Wiki. But the link to the latter also seems to be missing on the normal website(?). Hope it helps, Jeroen ___ 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] potential energy =nan
I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong? Rgds John _ Who's that on the Red Carpet? Play win glamorous prizes. http://club.live.com/red_carpet_reveal.aspx?icid=REDCARPET_hotmailtextlink3 ___ 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] Basic Query
Am Mittwoch, 20. Juni 2007 schrieb priyanka srivastava: I am currently involved in doing a lipid-peptide simulation under NPAT conditions. The way I have applied NPAT condition is as follows: ref_p = 0 1 compressibility = 0.0 4.5e-5 with semiisotropic? Although while performing analysis it shows that the x and y dimensions are constant but still I am not sure about the way I have applied NPAT. Could somone please tell me the basis behind it? If i am remembering correctly, this is what above values should do: first dimension is x-y second one is the z direction. Reference pressure is 1 for both (obviously makes sense) whereas compressibility set to 0 for x-y plane prevents box changes in x and y direction. So only z-direction remains for adjusting pressure. Another thing is I have used vdwtype: cutoff. But my intention is not to use the twin range cutoff at all!! In my case rlist = rcoulomb = rvdw, i.e. all three are same!! Is this alright? (the coulombtype = PME) Sorry, didn't get that part of your question. Can you post relevant parts of your mdp and specify it further? Chapter 7 says that parameters for PME are fourierspacing and pme_order, rcoulomb should not be used then. Cheers Martin ___ 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] potential energy =nan
Am Mittwoch, 20. Juni 2007 schrieb Sheyore Omovie: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong? If you're using SPC water, try to make it flexible. This helped me several times. Cheers Martin ___ 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] website problems
Jeroen van Bemmelen wrote: L.S., Just to let you guys know, I'm experiencing some problems with the www.gromacs.org website. E.g.: whenever I press the 'DOCUMENTATION' button on the top menu I get the related page, but not the related submenu on the left side. And whenever I press the 'News' button on the main menu on the left side I get an error: [error] Warning: Invalid argument supplied for foreach() in /data/gmx/www- gmx/administrator/components/com_sef/core/sef.mapper.php on line 431 Warning: Cannot modify header information - headers already sent by (output started at /data/gmx/www- gmx/administrator/components/com_sef/core/sef.mapper.php:431) in /data/gmx/www- gmx/administrator/components/com_sef/core/sef.resolver.php on line 609 The page you are trying to access does not exist. Please select a page from the main menu. [/error] I'm working on a Windows 2000 SP4 machine with IE 6.0 SP1. Emptying the internet cache didn't solve it. Also tried another, similar machine, but same problems. It seems to me the only way of getting to the online manpages for the gromacs utilities now is by using the search-option or via the Wiki. But the link to the latter also seems to be missing on the normal website(?). we're working on it. Hope it helps, Jeroen ___ 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. 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 4205 fax: 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
Re: [gmx-users] potential energy =nan
Sheyore Omovie wrote: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong? It's hard to tell from your description, since an energy minimization is not a simulation... but please try following this general scheme http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation 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] temperature..
dear all, i completed a simulation of copper nanoparticles.I want to observe the change in temp during the simulation.could u please help me in calculating the temperature of the system at the end of simulation. ___ 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..
abhishek sharma wrote: dear all, i completed a simulation of copper nanoparticles.I want to observe the change in temp during the simulation.could u please help me in calculating the temperature of the system at the end of simulation. ___ 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 g_energy -- 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 4205 fax: 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
Re: [gmx-users] temperature..
abhishek sharma wrote: dear all, i completed a simulation of copper nanoparticles.I want to observe the change in temp during the simulation.could u please help me in calculating the temperature of the system at the end of simulation. Very funny. This is the same type of question you asked on June 17, to which I replied here - http://www.gromacs.org/pipermail/gmx-users/2007-June/028053.html My reply is the same... read section 7.4 of the manual and *work out* which utility might be useful for you. You might even remember some of the other ones so that next time you don't have to search as hard. If you ever want to be any good in this field, you will have to work out how to read and learn independently. This is what a university degree should be teaching people. This email list is not a free consultancy service for asking simple questions that are easily covered in the manuals and tutorials. Our time is valuable, and you should respect that if you want some of it. 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] 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
Re: [gmx-users] Basic Query
Hie, Many thanks for your reply. Yes I have used semi-isotropic coupling. Another doubt is why only a value of 4.5e-5? I have used PME and have mentioned rcoulomb in the .mdp file too, which as is pointed out by you, has no meaning!! But does this mean that my mdp file is wrong? Because if PME does not use rcoulomb it shud simply ignore the value. Actually I do not want to use twin range cutoff. So, I have given rvdw = rlist. Is this alright? Portion of my mdp file looks like this: ; Electrostatics coulombtype = PME fourier_nx = 6.4 fourier_ny = 5.0 fourier_nz = 8.1 pme_order = 4 rcoulomb= 1.5 rvdw= 1.5 Also since I have not specified vdwtype in the mdp file, so it automatically takes Cut-off. regards, Pri... --- Martin Höfling [EMAIL PROTECTED] wrote: Am Mittwoch, 20. Juni 2007 schrieb priyanka srivastava: I am currently involved in doing a lipid-peptide simulation under NPAT conditions. The way I have applied NPAT condition is as follows: ref_p = 0 1 compressibility = 0.0 4.5e-5 with semiisotropic? Although while performing analysis it shows that the x and y dimensions are constant but still I am not sure about the way I have applied NPAT. Could somone please tell me the basis behind it? If i am remembering correctly, this is what above values should do: first dimension is x-y second one is the z direction. Reference pressure is 1 for both (obviously makes sense) whereas compressibility set to 0 for x-y plane prevents box changes in x and y direction. So only z-direction remains for adjusting pressure. Another thing is I have used vdwtype: cutoff. But my intention is not to use the twin range cutoff at all!! In my case rlist = rcoulomb = rvdw, i.e. all three are same!! Is this alright? (the coulombtype = PME) Sorry, didn't get that part of your question. Can you post relevant parts of your mdp and specify it further? Chapter 7 says that parameters for PME are fourierspacing and pme_order, rcoulomb should not be used then. Cheers Martin ___ 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 Pinpoint customers who are looking for what you sell. http://searchmarketing.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] Basic Query
priyanka srivastava wrote: I have used PME and have mentioned rcoulomb in the .mdp file too, which as is pointed out by you, has no meaning!! But does this mean that my mdp file is wrong? Because if PME does not use rcoulomb it shud simply ignore the value. As you'd see by reading sections 4.9 and 7.3.9 of the manual, Martin's statement isn't right. The grid dimensions are controlled by the two parameters he mentioned, but there are plenty of other parameters that influence PME. You're right, in that if mdp file parameters will be ignored then the value you use isn't relevant. Actually I do not want to use twin range cutoff. So, I have given rvdw = rlist. Is this alright? Yes, see section 4.6.3. This is only relevant for vdw since coulombtype = PME Portion of my mdp file looks like this: ; Electrostatics coulombtype = PME fourier_nx = 6.4 fourier_ny = 5.0 fourier_nz = 8.1 pme_order = 4 rcoulomb= 1.5 rvdw= 1.5 Assuming you got these values from somewhere sensible and that they're consistent with the force field you're using, then this will give you some numbers that have at least as good a chance of corresponding to reality as anything :-) Also since I have not specified vdwtype in the mdp file, so it automatically takes Cut-off. Set it specifically, so that you don't have to remember what the default is in a year's time. 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] grompp or parameter file problem?
Hello all! I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port. I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro. When running grompp: grompp -f em.mdp -c dna+solvent.gro -p dna+solvent.top -o out.tpr with the following em.mdp: - ; DNA energy minimization in water ; cpp = /lib/cpp -traditional define = include = -I/***/share/gromacs/top/ffamber99.itp constraints = none integrator = cg nsteps = 1000 ; ; ENERGY MINIZATION STUFF ; emtol = 2000 emstep = 0.01 nstcgsteep = 100 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I get the fatal error message: Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (genbox.gro, 32804) does not match topology (dick.top, 0) --- Top file has all includes and its tail looks: [ molecules ] ; Compound#mols Protein 1 SOL 10682 - Does somebody have similar problems? Has somebody solved them? I will appreciate any help! regards /anna ___ 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!
Hi, I wrote a program to calculate the tilt angle between a helix axis and the bilayer normal called g_tilt. It's available here http://condor.ebgm.jussieu.fr/~fuchs/download/. There you'll find also a program to calculate the azimuthal rotation (g_rotation). I plan to upload these contributions on the GROMACS website when I have time :-) Ciao, Patrick priyanka srivastava a écrit : 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] Umbrella sampling of a ligand inside a pore
First of all - Thank you very much for your thorough reply! I am having trouble defining the parameters for the simulations. As I understand, I should generate many starting structures, in which the position of the drug differ by, say, 0.5 Angstrom apart on the z axis. So let's say I have 30 starting structures (protein + drug + lipid bilayer + water). Be sure that you generate these carefully. Don't yank them all from one initial starting structure or your huge forces bay severly change the structure in some instances. A stepwise method of generation would be better. What I did was to position the ligand in the center of the protein pore, and consecutively move it by 0.5 steps along Z (both up and down until it reaches the bulk on both sides). In each step I re-center the ligands x,y inside the pore to avoid clashes (using nearby residues). Then, each of the generated structure is energy-minimized. Hope it's careful enough. how do I determine the best value for it? trial and error. You must have enough overlap to reduce WHAM errors. However, too much overlap and you will end up prolonging simulation time. But that's not too much of an issue if you have lots of cpus since it won't be wasted sampling. If you understand WHAM and can code yourself then you won't need to waste any data if you change force constants or nominal positions half-way through. Basically if you have tons of cpus then just overkill the overlap. If not, spread as many as you can and then make histograms of P(rx) vs. rx and measure overlap (where rx is your reaction coord. e.g. z) Then in places where there is not enough overlap you should do new simulations with umbrellas that are in intermediate positions. Don't like trial and error? I am sure there are better ways. Look into adaptive umbrella sampling. I'll probably perform trial and error before I move to more advanced methods. Do I have to optimize the force constant for each simulation or is it OK to use the same for all? Pulldim = Y Y N, since for each starting structure, the point is to see if it moves along x,y due to the forces acting on it by the protein. As I understand, since the ligand's z position is different in each starting structure, we can analyze it with WHAM and calculate the PMF. Does that sound right, or am I completely wrong? Completely wrong. Pick a reaction coordinate and then have different starting structures along that reaction coordinate and also harmonically restrain to that reaction coordinate. If the reaction coordinate that you want is xy then your starting structures should have the xy close to their Force=0 value. In this case either give all z the same value or whatever you want, but be sure to make sure that this has converged. If the reaction coordinate is z then as it moves along x y makes no sense since you won't get any information about this. That's the part I'm confused about. The reaction coordinate is definitely the z axis. That's why I have 30 different starting structures of the ligand along Z inside the pore. But when you configure pulldim=N N Y, you enable it to move only in the z-axis. So you won't see movements of the ligand in the xy plane inside the pore (surely the harmonic restraint of x and y wasn't the optimal x,y). So isn't it better to use the default pulldim=Y Y Y in that case? The confusing issue is that it seems we're already performing the pulling by generating overlapping starting structures, and the remaining question is what's the free energy when the ligand is around that specific Z (for each Z), yet still let it move freely within XY. The result of a simulation with the aforementioned parameters is that the ligand escapes the protein *into* the lipid environment, which doesn't make sense. When I use K1=10, the drug does not escape the pore. So I'm confused here. I thought K1=1000 was supposed to put more force on the drug to stay in its original position. Yes, larger Fc puts more force. But what happens depends on where 33.482 31.225 33.173 is. Your simulation is definately in error if the protein pore is at X=33.482, y=31.225 and a K1=100kJ/mol/nm^2 pulls it far away from that position. If so, are you sure that you don't have a negative sign in the force constant? Any help and ideas regarding why this is wrong? You are definately confused about z vs. xy and what is your reaction coordinate. I suspect that although you have ensured that z=33.173 is in your pore, you did not ensure that X=33.482, y=31.225 is in your pore. If this is true and you can't understand why that's a problem then you need to focus on the definition of a reaction coordinate. Now this feels stupid. I Forgot that gromacs uses nm units, and gave it coordinates in Angstroms. Thanks again, Hadas. If this is not the case and you can't figure it out, then reduce your system to something
Re: [gmx-users] Inclusion of an angle-angle cross term?
Lee-Ping wrote: Hi there, I'm working on fitting some force field parameters to a batch of ab-initio single-point force calculations, and the fit still needs improvement. I'm thinking of including an angle-angle cross term in my custom force field, but so far I haven't found that GROMACS can implement this. I think that five atom labels and three parameters are needed to describe such an interaction; can GROMACS do this right now? Thanks. I don't think so... but check out src/gmxlib/ifunc.c and src/gmxlib/bondfree.c for what there is there. 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
Re: [gmx-users] grompp or parameter file problem?
What's the name for DNA under [ moleculetype ] in your top file? Another question is: have you included ffamber_tip3p.itp? Probably you need to post excerpt of your topology here if you are not sure about your answers towards above two questions. Regards, Yang Ye - Original Message From: Anna Reymer [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, June 20, 2007 10:57:28 PM Subject: [gmx-users] grompp or parameter file problem? Hello all! I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port. I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro. When running grompp: grompp -f em.mdp -c dna+solvent.gro -p dna+solvent.top -o out.tpr with the following em.mdp: - ; DNA energy minimization in water ; cpp = /lib/cpp -traditional define = include = -I/***/share/gromacs/top/ffamber99.itp constraints = none integrator = cg nsteps = 1000 ; ; ENERGY MINIZATION STUFF ; emtol = 2000 emstep = 0.01 nstcgsteep = 100 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I get the fatal error message: Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (genbox.gro, 32804) does not match topology (dick.top, 0) --- Top file has all includes and its tail looks: [ molecules ] ; Compound#mols Protein 1 SOL 10682 - Does somebody have similar problems? Has somebody solved them? I will appreciate any help! regards /anna ___ 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] potential energy =nan
Hi Mark, I'm sorry, I assume you'll understand that I've carried out all the steps before an EM run. David said is because the coordinates are on top of each other, I'll appreciate any more specific advice on how to fix this. Meanwhile, I'll try Martin's advice on making the water flexible. Rgds John From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 23:09:03 +1000 Sheyore Omovie wrote: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong? It's hard to tell from your description, since an energy minimization is not a simulation... but please try following this general scheme http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation 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 _ Picture this share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHMloc=us ___ 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] potential energy =nan
Hi, I figured it might be neccessary to show my *.top file and coordinate file (b4 solvation) so I could easily get help. Rgds John ; File 'twopoly.top' was generated ; By user: sjomovie (1028) ; On host: bmp041.biophysics.net ; At date: Tue Jun 19 23:12:16 2007 ; ; This is your topology file ; Great Red Oystrich Makes All Chemists Sane ; ; Include forcefield parameters #include ffG43a1.itp ; Include chain topologies #include twopoly_B.itp #include twopoly_A.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 Great Red Oystrich Makes All Chemists Sane in water [ molecules ] ; Compound#mols Protein_B 1 Protein_A 1 SOL 314583 TITLE Great Red Oystrich Makes All Chemists Sane REMARKTHIS IS A SIMULATION BOX CRYST1 10.2665.7232.981 90.00 90.00 90.00 P 1 1 MODEL1 ATOM1 N ALA B 1 -0.677 -1.23 -0.491 1 0 ATOM2 H1 ALA B 1 -1.667 -1.089 -0.491 1 0 ATOM3 H2 ALA B 1 -0.414 -1.744 -1.307 1 0 ATOM4 H3 ALA B 1 -0.414 -1.744 0.325 1 0 ATOM5 CA ALA B 1 -0.001 0.064 -0.491 1 0 ATOM6 CB ALA B 1 -0.509 0.856 0.727 1 0 ATOM7 C ALA B 1 1.499 -0.11 -0.491 1 0 ATOM8 O ALA B 1 2.065 -0.922 0.251 1 0 ATOM9 N GLY B 2 2.311 0.711 -1.41 0 ATOM10 H GLY B 2 1.979 1.399 -2.045 1 0 ATOM11 CA GLY B 2 3.7 0.321 -1.173 1 0 ATOM12 C GLY B 2 4.606 1.528 -1.169 1 0 ATOM13 O GLY B 2 4.515 2.418 -2.019 1 0 ATOM14 N ALA B 3 5.629 1.648 -0.12 1 0 ATOM15 H ALA B 3 5.805 1.002 0.622 1 0 ATOM16 CA ALA B 3 6.336 2.899 -0.378 1 0 ATOM17 CB ALA B 3 5.719 3.979 0.528 1 0 ATOM18 C ALA B 3 7.821 2.735 -0.164 1 0 ATOM19 O1 ALA B 3 8.258 1.505 0.219 1 0 ATOM20 O2 ALA B 3 8.599 3.831 -0.372 1 0 ATOM21 N ALA A 4 -0.677 -1.23 -0.491 1 0 ATOM22 H1 ALA A 4 -1.667 -1.089 -0.491 1 0 ATOM23 H2 ALA A 4 -0.414 -1.744 -1.307 1 0 ATOM24 H3 ALA A 4 -0.414 -1.744 0.325 1 0 ATOM25 CA ALA A 4 -0.001 0.064 -0.491 1 0 ATOM26 CB ALA A 4 -0.509 0.856 0.727 1 0 ATOM27 C ALA A 4 1.499 -0.11 -0.491 1 0 ATOM28 O ALA A 4 2.065 -0.922 0.251 1 0 ATOM29 N ALA A 5 2.311 0.711 -1.41 0 ATOM30 H ALA A 5 1.979 1.399 -2.045 1 0 ATOM31 CA ALA A 5 3.7 0.321 -1.173 1 0 ATOM32 CB ALA A 5 4.079 -0.705 -2.254 1 0 ATOM33 C ALA A 5 4.606 1.529 -1.169 1 0 ATOM34 O ALA A 5 4.515 2.421 -2.021 1 0 ATOM35 N ALA A 6 5.629 1.648 -0.119 1 0 ATOM36 H ALA A 6 5.806 1.001 0.623 1 0 ATOM37 CA ALA A 6 6.335 2.9 -0.377 1 0 ATOM38 CB ALA A 6 5.718 3.979 0.529 1 0 ATOM39 C ALA A 6 7.821 2.736 -0.163 1 0 ATOM40 O1 ALA A 6 8.258 1.506 0.219 1 0 ATOM41 O2 ALA A 6 8.599 3.832 -0.37 1 0 TER ENDMDL From: Sheyore Omovie [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 11:44:32 -0500 Hi Mark, I'm sorry, I assume you'll understand that I've carried out all the steps before an EM run. David said is because the coordinates are on top of each other, I'll appreciate any more specific advice on how to fix this. Meanwhile, I'll try Martin's
Re: [gmx-users] potential energy =nan
Sheyore Omovie wrote: Hi Mark, I'm sorry, I assume you'll understand that I've carried out all the steps before an EM run. David said is because the coordinates are on top of each other, I'll appreciate any more specific advice on how to fix this. use a molecule viewer Meanwhile, I'll try Martin's advice on making the water flexible. Rgds John From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 23:09:03 +1000 Sheyore Omovie wrote: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong? It's hard to tell from your description, since an energy minimization is not a simulation... but please try following this general scheme http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation 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 _ Picture this – share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHMloc=us ___ 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. 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 4205 fax: 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
Re: [gmx-users] Basic Query
priyanka srivastava wrote: Hie, Many thanks for your reply. Yes I have used semi-isotropic coupling. Another doubt is why only a value of 4.5e-5? I have used PME and have mentioned rcoulomb in the .mdp file too, which as is pointed out by you, has no meaning!! But does this mean that my mdp file is wrong? Because if PME does not use rcoulomb it shud simply ignore the value. Actually I do not want to use twin range cutoff. So, I have given rvdw = rlist. Is this alright? Portion of my mdp file looks like this: ; Electrostatics coulombtype = PME fourier_nx = 6.4 fourier_ny = 5.0 fourier_nz = 8.1 these numbers should be integers pme_order = 4 rcoulomb= 1.5 rvdw= 1.5 Also since I have not specified vdwtype in the mdp file, so it automatically takes Cut-off. regards, Pri... --- Martin Höfling [EMAIL PROTECTED] wrote: Am Mittwoch, 20. Juni 2007 schrieb priyanka srivastava: I am currently involved in doing a lipid-peptide simulation under NPAT conditions. The way I have applied NPAT condition is as follows: ref_p = 0 1 compressibility = 0.0 4.5e-5 with semiisotropic? Although while performing analysis it shows that the x and y dimensions are constant but still I am not sure about the way I have applied NPAT. Could somone please tell me the basis behind it? If i am remembering correctly, this is what above values should do: first dimension is x-y second one is the z direction. Reference pressure is 1 for both (obviously makes sense) whereas compressibility set to 0 for x-y plane prevents box changes in x and y direction. So only z-direction remains for adjusting pressure. Another thing is I have used vdwtype: cutoff. But my intention is not to use the twin range cutoff at all!! In my case rlist = rcoulomb = rvdw, i.e. all three are same!! Is this alright? (the coulombtype = PME) Sorry, didn't get that part of your question. Can you post relevant parts of your mdp and specify it further? Chapter 7 says that parameters for PME are fourierspacing and pme_order, rcoulomb should not be used then. Cheers Martin ___ 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 Pinpoint customers who are looking for what you sell. http://searchmarketing.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 -- 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 4205 fax: 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
Re: [gmx-users] Inclusion of an angle-angle cross term?
Lee-Ping wrote: Hi there, I'm working on fitting some force field parameters to a batch of ab-initio single-point force calculations, and the fit still needs improvement. I'm thinking of including an angle-angle cross term in my custom force field, but so far I haven't found that GROMACS can implement this. I think that five atom labels and three parameters are needed to describe such an interaction; can GROMACS do this right now? Thanks. It won't work out of the box, but in principle it is not very difficult. Appendix B4 describes which files to modify. -- 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 4205 fax: 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
Re: [gmx-users] Inclusion of an angle-angle cross term?
Lee-Ping wrote: Hi there, I'm working on fitting some force field parameters to a batch of ab-initio single-point force calculations, and the fit still needs improvement. I'm thinking of including an angle-angle cross term in my custom force field, but so far I haven't found that GROMACS can implement this. I think that five atom labels and three parameters are needed to describe such an interaction; can GROMACS do this right now? Thanks. - Lee-Ping Wang and table 5.4 shows that there already is a 5 atom interaction. Otherwise this is more a developer question. -- 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 4205 fax: 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
Re: [gmx-users] website problems
Jeroen van Bemmelen wrote: L.S., Just to let you guys know, I'm experiencing some problems with the www.gromacs.org website. E.g.: whenever I press the 'DOCUMENTATION' button on the top menu I get the related page, but not the related submenu on the left side. And whenever I press the 'News' button on the main menu on the left side I get an error: it should be fine again now. please let us know if there are further problems. -- 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 4205 fax: 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
Re: [gmx-users] Basic Query
Am Mittwoch, 20. Juni 2007 schrieb Mark Abraham: As you'd see by reading sections 4.9 and 7.3.9 of the manual, Martin's statement isn't right. The grid dimensions are controlled by the two parameters he mentioned, but there are plenty of other parameters that influence PME. Oh, I didn't checked 4.9. Then of course rlist makes sense too for coulomb interactions with PME. Set it specifically, so that you don't have to remember what the default is in a year's time. ... and look in your own mdp file before making statements :-) Best Martin ___ 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] Umbrella sampling of a ligand inside a pore
What I did was to position the ligand in the center of the protein pore, and consecutively move it by 0.5 steps along Z (both up and down until it reaches the bulk on both sides). In each step I re-center the ligands x,y inside the pore to avoid clashes (using nearby residues). Then, each of the generated structure is energy-minimized. Hope it's careful enough. Sounds fine. Although I am not sure what you mean by move it If you are translating it and then you are going to solvate each system independently later then that all sounds proper. I'll probably perform trial and error before I move to more advanced methods. Do I have to optimize the force constant for each simulation or is it OK to use the same for all? Either is ok (as long as your WHAM implementation allows different Fc values (most do, but be sure that it does). Start with the same for all and if you are missing sampling in some region then you can add a new umbrella or perhaps adjust a force constant. I find it easier to predict what will happen when I add another umbrella. That's the part I'm confused about. The reaction coordinate is definitely the z axis. That's why I have 30 different starting structures of the ligand along Z inside the pore. But when you configure pulldim=N N Y, you enable it to move only in the z-axis. So you won't see movements of the ligand in the xy plane inside the pore (surely the harmonic restraint of x and y wasn't the optimal x,y). So isn't it better to use the default pulldim=Y Y Y in that case? This is not true: You enable it to move only in the z-axis What you do with NNY is *force* it to move in the z-axis but the x and y can still move it's just that they find their own equilibrium. The confusing issue is that it seems we're already performing the pulling by generating overlapping starting structures, and the remaining question is what's the free energy when the ligand is around that specific Z (for each Z), yet still let it move freely within XY. Exactly, but to do that you need to have pulldim=NNY. Here's why: The accuracy and precision of computationally-derived properties are dependent not only on complete sampling of the relevant conformational space, but also on the presence of sufficient transitions between local minima on the energy landscape so as to provide information on the density of states. This implies that unrestrained computer simulations can adequately measure only those processes that occur at periods much less than the time of data acquisition. And yet, if the relevant motions of largest period may be determined and exhaustively sampled by means of a biasing potential, the time of data acquisition required from each individual simulation is now related to the motions of the second largest period. In this case you have (correctly) selected the z axis as the reaction coordinate along which the relevant ion motions of largest period will occur. You now complete a variety of simulations at varying positions along z, allowing x and y to reach their own equilibrium. If you're still confused (and even if you aren't) then try some of the online talks by David Mobley (http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial) or Alan Grossfield (http://dasher.wustl.edu/alan/talks/wham_talk.pdf) or there are lots of others. Hope that helps, I am about all tapped out on general suggestions for this topic. Chris. ___ 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] new to gromacs
vijay kumar wrote: hi everyone I am new to gromacs software all i need to do is submit my project in 2 months first thing i am able to do is work with demos ,i did them perfectly but the thing is now i need to edit the water molecule pdb file and start a new project i.e. now i need to create a new pdb file with 20 molecules of water ,generate a new topology file and define mdp parameters ,can any one please mail me the procedure to start from the basics and where can i find the details of this in the Gromacs.org the doubts is edit a pdb file store and retrieve it to command prompt define mdp parameters file and use for the program and run the simulation please send me step by step as given in the demo of water molecule you want to read chap 5 of the manual you can do all this with a text editor. Looking for people who are YOUR TYPE? Find them at in.groups.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 -- 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 4205 fax: 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
Re: [gmx-users] new to gromacs
vijay kumar wrote: hi everyone I am new to gromacs software all i need to do is submit my project in 2 months first thing i am able to do is work with demos ,i did them perfectly but the thing is now i need to edit the water molecule pdb file and start a new project i.e. now i need to create a new pdb file with 20 molecules of water ,generate a new topology file and define mdp parameters ,can any one please mail me the procedure to start from the basics and where can i find the details of this in the Gromacs.org the doubts is edit a pdb file store and retrieve it to command prompt define mdp parameters file and use for the program and run the simulation please send me step by step as given in the demo of water molecule You will find some useful material in the links from this page http://wiki.gromacs.org/index.php/Beginners You should also follow David's suggestions. 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] rtp entry
Hi Mark, Thank you for your valuable suggestion.I did go through the manual, but I want to confirm if I need to add the atom CA in the ffoplsaa.rtp file, and if so I am not sure what the appropiate Type of angles, Type of proper dihedrals, Type of improper dihedrals I have to enter. If I choose the force field with option 0 then it gives me an error saying residue AIB not found in residue topology. Any help would be highly appreciated. Thanks, Aj Mark Abraham [EMAIL PROTECTED] wrote: ASHWINI JAYAPRAKASH wrote: Hi, I am a new gromacs user and have problems creating a topology file using the pdb2gmx command for simulating a six helix bundled alamethecin in lipid bilayer. when I use the command : pdb2gmx -f almN6start -o almN6start.gro -p almN6start.top I get the error : Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2gmx.c, line: 393 Fatal error: Atom CA in residue ACE 1 not found in rtp entry with 6 atoms while sorting atoms This means what it says. pdb2gmx is finding a CA atom in an ACE residue in your coordinate file that it can't reconcile with the .rtp entry for ACE for the force field you're using. If this doesn't make any sense, you should read chapter five of the manual thoroughly. Probably the first four chapters are also worth reading too. - Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online.___ 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:Shear viscosity/bulk viscosity
[EMAIL PROTECTED] wrote: Dear Gromacs Users, When I use the command g_energy_d -vis -f *.edr files such as, evisco.xvg and visco.xvg are generated. evisco.xvg have 4 columns and viso.xvg has 2 colums. Can you please let me know what they are, as I failed to find the explanations in 6.5 of the manual and the paper published in the Journal of chemical physics 116:209-217, 2002. Thanks for letting us know how you've tried to solve the problem. Do the comments on the top of the .xvg file clarify this? 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
