[gmx-users] g_h2order problem
Hello, gmx-users， my system has just 2827 water molecules, but the g_h2order command told me that there are more than 2807 waters in each slice. there are only one group in my index file and in O H H sequence. why? the results are as follows: :-) G R O M A C S (-: Go Rough, Oppose Many Angry Chinese Serial killers :-) VERSION 3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_h2order (-: Option Filename Type Description -f 10ns.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb -n order_h2o.ndx InputIndex file -nm index.ndx Input, Opt. Index file -sbso20md.tpr InputGeneric run input: tpr tpb tpa xml -o order.xvg Output xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 2600 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -d string Z Take the normal on the membrane in direction X, Y or Z. -slint100 Calculate order parameter as function of boxlength, dividing the box in #nr slices. Reading file bso20md.tpr, VERSION 3.3 (single precision) Group 0 ( OW_HW1_HW2) has 8481 elements There is one group in the index Reading frame 0 time 2600.000 Box divided in 100 slices. Initial width o f slice: 0.103958 Reading frame1550 time 9980.000 Read trajectory. Printing parameters to file 91697 waters in slice 0 91534 waters in slice 1 91403 waters in slice 2 91630 waters in slice 3 90943 waters in slice 4 91577 waters in slice 5 91589 waters in slice 6 91367 waters in slice 7 91485 waters in slice 8 91641 waters in slice 9 91528 waters in slice 10 91599 waters in slice 11 91867 waters in slice 12 92253 waters in slice 13 92324 waters in slice 14 92318 waters in slice 15 91075 waters in slice 16 87944 waters in slice 17 82109 waters in slice 18 75151 waters in slice 19 67429 waters in slice 20 57285 waters in slice 21 42809 waters in slice 22 26212 waters in slice 23 12391 waters in slice 24 4453 waters in slice 25 1129 waters in slice 26 204 waters in slice 27 29 waters in slice 28 3 waters in slice 29 0 waters in slice 30 No water in slice 30 0 waters in slice 31 No water in slice 31 0 waters in slice 32 No water in slice 32 0 waters in slice 33 No water in slice 33 0 waters in slice 34 No water in slice 34 0 waters in slice 35 No water in slice 35 0 waters in slice 36 No water in slice 36 0 waters in slice 37 No water in slice 37 0 waters in slice 38 No water in slice 38 0 waters in slice 39 No water in slice 39 0 waters in slice 40 No water in slice 40 0 waters in slice 41 No water in slice 41 0 waters in slice 42 No water in slice 42 0 waters in slice 43 No water in slice 43 0 waters in slice 44 No water in slice 44 0 waters in slice 45 No water in slice 45 0 waters in slice 46 No water in slice 46 0 waters in slice 47 No water in slice 47 0 waters in slice 48 No water in slice 48 0 waters in slice 49 No water in slice 49 0 waters in slice 50 No water in slice 50 0 waters in slice 51 No water in slice 51 0 waters in slice 52 No water in slice 52 0 waters in slice 53 No water in slice 53 0 waters in slice 54 No water in slice 54 0 waters in slice 55 No water in slice 55 0 waters in slice 56 No water in slice 56 0 waters in slice 57 No water in slice 57 0 waters in slice 58 No water in slice 58 0 waters in slice 59 No water in slice 59 0 waters in slice 60 No water in slice 60 0 waters in slice 61 No water in slice 61 0 waters in slice 62 No water in slice 62 1 waters in slice 63 0 waters in slice 64 No water in slice 64 1 waters in slice 65 1 waters in slice 66 17 waters in slice 67 146 waters in slice 68 927 waters in slice 69
Re: [gmx-users] forcefield
Dear Hadi, You also forgot to define "better". What do you want to learn from that peptide? Do you need all hydrogens for that? Or could you do without? Also consider that the generality of the question phrased does usually not trigger people in a way desired for reply. It sounds a bit like "I've got some homework, but would like you to do it for me". Study the manual and papers on MD, in particular of small peptides and force fields. Now there's a bit of homework ;) Cheers, TsjerkOn 5/23/06, Mark Abraham <[EMAIL PROTECTED]> wrote: hadi behzadi wrote:> Hi all of users>> For HHAHHAADAAHHAAD peptide what kinde of force field is better ?I don't know, but I could tell you the answer immediately forHHAHAHADAAHHAAD peptide :-P General force fields are parameterized to be reasonable over a range ofsystems. The overview of force fields in the GROMACS manual is good, andyou should refer to the papers that describe them for more detail. Mark___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ 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] ffAMBER ports updated
Hi, We have updated the ffAMBER website to include AMBER ports for v3.3.1 and also incorporated the AMBER-03 force field of Duan et al. in all ffAMBER ports (v3.1.4 thru v3.3.1). Please visit http://folding.stanford.edu/ffamber/ for more info. Enjoy! Eric J. Sorin Pande Group Stanford University Department of Chemistry ___ 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] forcefield
hadi behzadi wrote: Hi all of users For HHAHHAADAAHHAAD peptide what kinde of force field is better ? I don't know, but I could tell you the answer immediately for HHAHAHADAAHHAAD peptide :-P General force fields are parameterized to be reasonable over a range of systems. The overview of force fields in the GROMACS manual is good, and you should refer to the papers that describe them for more detail. Mark ___ 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] Beware of your interconnect hardware
Jason O'Young wrote: Hey All, Not too long ago I posted about my problems with processes freezing (just to refresh, I am running two dual-core nodes for a total of four processes). I managed to remedy the problem by removing the Dell PowerConnect 2708 Gigabit switch and replacing it with a simple crossover cable. Ever since then, the system has been running rock solid. Are there actually issues with switch hardware with Gromacs? I used to think that these things were pretty much fool proof. I spent about a month trying to fix what I perceived as a Linux issue. Please be careful to differentiate a switch hardware problem from a Linux OS problem from an MPI problem from a GROMACS problem. The observation of processes freezing could be caused by a failure of any of those systems, and it is unfair to blame GROMACS for problems at a hardware level... Your question above is a bit like someone on a motoring mailing list asking whether Mercedes-Benz cars have a problem with tires because you keep skidding off the road in your Merc. The problem could be with your technique as the driver, the road conditions, the speed you're driving at, the tires, or various bits of the car. Mark ___ 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] Simulating crystalls
David van der Spoel wrote: Gale, Ella wrote: Thanks for the advice, but my force-field has no charges and hence no coulomb potential, so I want the atoms to interact with itself via the Van der Waals functions. I'm using 3.2.1 at the moment and there is no option to use any of the Ewald summation techniques. Is this something that has been added in the most recent version? Ewald variant are only for Coulomb so far. You can use a normal cutoff or a shifted cutoff. One or two of the early PME papers describe implementation details for LJ PME, but I am not immediately aware of a modern MD code that implements it. If you want it, shop around. Mark ___ 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] Simulating crystalls
Gale, Ella wrote: Thanks for the advice, but my force-field has no charges and hence no coulomb potential, so I want the atoms to interact with itself via the Van der Waals functions. I'm using 3.2.1 at the moment and there is no option to use any of the Ewald summation techniques. Is this something that has been added in the most recent version? Ewald variant are only for Coulomb so far. You can use a normal cutoff or a shifted cutoff. -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Tue 5/23/2006 2:19 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Simulating crystalls Gale, Ella wrote: > > Hi, > > I was wondering is it possible to simulate a crystall by just simulating > a unit cell in GROMACS? I want the molecule to be able to interact with > the images of itself, but I don't seem to be able to set rlist, rvdw or > rcoulomb any larger than half the unit cell size, which explicitly > prevents my molecule from interacting with itself. Use Ewald, or preferably particle-mesh Ewald (PME) for crystalline systems. That was what they were invented for. Mark ___ 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 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 -- 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 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] Beware of your interconnect hardware
Jason O'Young wrote: Hey All, Not too long ago I posted about my problems with processes freezing (just to refresh, I am running two dual-core nodes for a total of four processes). I managed to remedy the problem by removing the Dell PowerConnect 2708 Gigabit switch and replacing it with a simple crossover cable. Ever since then, the system has been running rock solid. Are there actually issues with switch hardware with Gromacs? I used to think that these things were pretty much fool proof. I spent about a month trying to fix what I perceived as a Linux issue. That poses a question I have to all of you. Is there a particular brand or model of switch you recommend? Eventually I would like to add another node to the system! If you read the Rocks mailing lists (Cluster Linux Distro) you will be surprised. Dell switches are considered to be crap. Get HP instead (if your contract allows it...). Go to www.rocksclusters.org for more info. Thanks, Jason ___ 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 -- 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 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] Ions close to protein
David Mobley wrote: Joanne, >When I add ions to my system to neutralise it some are placed quite close to the protein (even when using random) and in other cases during simualtions I have seen ions move into the protein, is this normal/okay and are there any ways of keeping these ions away from the protein? In terms of keeping them away from the protein, not too sure. But I think it is right to be nervous about ions that move into your protein. These could have long correlation times. Depending on how long the correlation times are, you might need to run longer to get adequate sampling. On the other hand, if your salt concentration is reasonable, you might have enough ions that this behavior will appropriately average out, especially if correlation times are relatively short. Probably, the overall answer to whether this is okay depends on what question you are trying to ask. My personal opinion is that ions are a whole can of worms that is mostly unopened so far, but sooner or later someone will have to open it and it will be messy (long correlation times, bad parameters, and strongly influence certain things). But perhaps I'm just being pessimistic. And, in fairness, I should say that so far I've decided just to ignore the issue, because I don't want to be the guy who opens the can of worms. OK, better show a glimpse of what's in the can then... We are finishing a paper about this stuff, and the conclusion is: no problem as long as your simulations are reasonably long and you use PME. Charged sidechains have *on average* half a counterion in our tests. A real problem may be that force fields are not adapted to having realistic ionic strength, and hence you might influence protein stability by introducing. This is very hard to prove however. -- 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 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] Ions close to protein
Joanne, >When I add ions to my system to neutralise it some are placed quite close to the protein (even when using random) and in other cases during simualtions I have seen ions move into the protein, is this normal/okay and are there any ways of keeping these ions away from the protein? In terms of keeping them away from the protein, not too sure. But I think it is right to be nervous about ions that move into your protein. These could have long correlation times. Depending on how long the correlation times are, you might need to run longer to get adequate sampling. On the other hand, if your salt concentration is reasonable, you might have enough ions that this behavior will appropriately average out, especially if correlation times are relatively short. Probably, the overall answer to whether this is okay depends on what question you are trying to ask. My personal opinion is that ions are a whole can of worms that is mostly unopened so far, but sooner or later someone will have to open it and it will be messy (long correlation times, bad parameters, and strongly influence certain things). But perhaps I'm just being pessimistic. And, in fairness, I should say that so far I've decided just to ignore the issue, because I don't want to be the guy who opens the can of worms. David > > This is normal in the sense that it certainly happens in the real systems. The fact is that you probably don't want the ions to go mess up with your protein !! One solution: 1)order your solent in function of the distance to the protein, trjorder does this. 2)generate an index where you separate your solvent into the close and far from the protein. 3) then use genion giving this index and choose the index far from protein. Note that this won't ovoid the contact ion-protein during your simulation !! XAvier -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel: +31-503634329 Fax: +31-503634398 email: [EMAIL PROTECTED] web-page: http://md.chem.rug.nl/~periole -- ___ 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 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] Beware of your interconnect hardware
Hey All, Not too long ago I posted about my problems with processes freezing (just to refresh, I am running two dual-core nodes for a total of four processes). I managed to remedy the problem by removing the Dell PowerConnect 2708 Gigabit switch and replacing it with a simple crossover cable. Ever since then, the system has been running rock solid. Are there actually issues with switch hardware with Gromacs? I used to think that these things were pretty much fool proof. I spent about a month trying to fix what I perceived as a Linux issue. That poses a question I have to all of you. Is there a particular brand or model of switch you recommend? Eventually I would like to add another node to the system! Thanks, Jason ___ 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] Simulating crystalls
Title: RE: [gmx-users] Simulating crystalls Thanks for the advice, but my force-field has no charges and hence no coulomb potential, so I want the atoms to interact with itself via the Van der Waals functions. I'm using 3.2.1 at the moment and there is no option to use any of the Ewald summation techniques. Is this something that has been added in the most recent version? -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Tue 5/23/2006 2:19 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Simulating crystalls Gale, Ella wrote: > > Hi, > > I was wondering is it possible to simulate a crystall by just simulating > a unit cell in GROMACS? I want the molecule to be able to interact with > the images of itself, but I don't seem to be able to set rlist, rvdw or > rcoulomb any larger than half the unit cell size, which explicitly > prevents my molecule from interacting with itself. Use Ewald, or preferably particle-mesh Ewald (PME) for crystalline systems. That was what they were invented for. Mark ___ gmx-users mailing list gmx-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 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] forcefield
Hi all of users For HHAHHAADAAHHAAD peptide what kinde of force field is better ? New Yahoo! Messenger with Voice. Call regular phones from your PC and save big.___ 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] POPC simulation
Hi Steffen,Thanks very much for the prompt reply. i made the changes as mentioned such that my popc.top looks like this :-#include "ffgmx.itp"#include "lipid.itp"#include "popc.itp" #include "ffgmx2nb.itp"#include "ffgmx2bon.itp"however is still get the same message "Fatal error: Bonded/nonbonded atom type 'LP2' not found!". i forgot to mention one thing in my earlier mail that the ffgmx.atp file provided with originally from GROMACS , i replaced the contents of it by the contents present in the ffgmx.atp file present in the ffgmx_lipids folder as downloaded from the Gromacs website. my understanding is this shouldn;t cause the problem since the orinigal ffgmx.atp file ( as provided by gromacs) doesn;t contain all the atom types. in fact when i compared the both files i found that the ffgmx.atp file (from ffgmx_lipids folder ) has the following extra entries which were required for the lipid simulation. i am kind of confused as to where i am committig the mistake. plz help. thanks. Arindam GangulyHi Arindam,you've simply got to switch two lines in the *.top file: lipid.itp hasto be called by the topology before popc.itp, as it contains theinformation on atomtypes for GROMACS. So: #include "lipid.itp"#include "popc.itp"should work just fine.GreetingsSteffen ___ 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] Ions close to protein
Joanne Hanna wrote: Hi When I add ions to my system to neutralise it some are placed quite close to the protein (even when using random) and in other cases during simualtions I have seen ions move into the protein, is this normal/okay and are there any ways of keeping these ions away from the protein? This is normal in the sense that it certainly happens in the real systems. The fact is that you probably don't want the ions to go mess up with your protein !! One solution: 1)order your solent in function of the distance to the protein, trjorder does this. 2)generate an index where you separate your solvent into the close and far from the protein. 3) then use genion giving this index and choose the index far from protein. Note that this won't ovoid the contact ion-protein during your simulation !! XAvier -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel: +31-503634329 Fax: +31-503634398 email: [EMAIL PROTECTED] web-page: http://md.chem.rug.nl/~periole -- ___ 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] Ions close to protein
Joanne Hanna wrote: Hi When I add ions to my system to neutralise it some are placed quite close to the protein (even when using random) and in other cases during simualtions I have seen ions move into the protein, is this normal/okay and are there any ways of keeping these ions away from the protein? this is normal. Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [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 -- 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 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] Ions close to protein
Hi When I add ions to my system to neutralise it some are placed quite close to the protein (even when using random) and in other cases during simualtions I have seen ions move into the protein, is this normal/okay and are there any ways of keeping these ions away from the protein? Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [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
Re: [gmx-users] Simulating crystalls
Gale, Ella wrote: Hi, I was wondering is it possible to simulate a crystall by just simulating a unit cell in GROMACS? I want the molecule to be able to interact with the images of itself, but I don't seem to be able to set rlist, rvdw or rcoulomb any larger than half the unit cell size, which explicitly prevents my molecule from interacting with itself. Use Ewald, or preferably particle-mesh Ewald (PME) for crystalline systems. That was what they were invented for. Mark ___ 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] Suggestions awaited
Dear all, I wanted to calculate the angle joining the normal to the tyrosine ring and the vector joining the succeeding residue. I tried using the g_sgangle option in gromacs to calculate the angle between these 2 groups, and the distance between the 2 grps but as soon as I selected the first grp frm the index file all the calculations were performed according to the first slection. The option to select the second grp frm the index file was not asked. Please help, Richa __ 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] FF choice.
David van der Spoel wrote: are you sure you want this force field by the way? I apologize if it is a FAQ. I'd like to make some MD simulations of a small molecule (cinchonidine), changing solvents and other stuff. Obviously, I've to compute a new topology for the molecule... Then, how can I choose the best FF, considering that gromacs FF is deprecated in gromacs 3.3? I computed the topology using prodrg, then I chose the gromacs FF because I used it some time ago for proteins. Are there other tools to compute a topology from, for example, a Z-matrix file? Thanks, Gianluca ___ 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] Simulating crystalls
Title: Simulating crystalls Hi, I was wondering is it possible to simulate a crystall by just simulating a unit cell in GROMACS? I want the molecule to be able to interact with the images of itself, but I don't seem to be able to set rlist, rvdw or rcoulomb any larger than half the unit cell size, which explicitly prevents my molecule from interacting with itself. Any ideas? Regards Ella Gale ___ 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] PBC and large hydrogen-bonded molecules
Hi,On 5/23/06, Mark Abraham <[EMAIL PROTECTED]> wrote: [EMAIL PROTECTED] wrote:> Hello fellow Gromacs-users,>> Today I was extracting PDB snapshots from a solvated DNA 12mer simulation trajectory.> When I went to view the snapshots, I saw that one of the DNA strands suddenly jumped > some nanometers away from its partner during certain frames. I remembered that there was> a note about fixing this artifact in the trjconv documentation, and soon found that the> -whole or -nojump options produced an easier-to-view snapshot series. Well done. Hear, hear! :) The simplest hypothesis for these images is that the visualisationprogram is placing the first atom it finds in each molecule inside the box and the rest of it consistent with that placement. More visuallyappealing might be an algorithm that located the center-of-massinside... shrug. Playing with the trjconv options before thevisualisation program gets into the mix may help here. Mark In fact, it is Gromacs which uses the first atom to decide in which box the molecule should be located during MD. But ALWAYS think of the simulation system as an infinite tiling of simulation unit cells. It doesn't matter a bit how you choose your single simulation cell from that infinite system.., except for visualization. Cheers, Tsjerk -- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands +31 50 363 4336 ___ 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] tbpconv
Magnus Andersson wrote: Hi, I used tbpconv to restart a crashed run. This will result in 2 separate .xtc and .trr files. How can I use for instance g_rdf on these files. Is there some way to fuse them? trjcat - there's a nice section in the GROMACS manual that lists the function of all the utilities in a one-liner... have a read. Mark ___ 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] tbpconv
Hi, I used tbpconv to restart a crashed run. This will result in 2 separate .xtc and .trr files. How can I use for instance g_rdf on these files. Is there some way to fuse them? /Magnus Andersson ___ 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] POPC simulation
Hi Arindam, you've simply got to switch two lines in the *.top file: lipid.itp has to be called by the topology before popc.itp, as it contains the information on atomtypes for GROMACS. So: #include "lipid.itp" #include "popc.itp" should work just fine. Greetings Steffen -- 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
