Re: [gmx-users] the warning about the -rerun
It seems that your are fine for the energies but the properties mentioned will be wrong. On Jun 30, 2009, at 4:48 AM, Jinyao Wang wrote: hi,gmx-users， I want to calculate the interaction energy between two group. So I modify the .mdp file as follows: energygrps = Protein sol and make tpr file: grompp -f md.mdp -c out.gro -p topol.top -o rerun.tpr -n index.ndx mdrun -rerun md.trr -s rerun.tpr -o rerun.trr -c rerun.gro -e rerun.edr -g rerun.log It gives warings: WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. How can I deal with the warning? Jinyao Wang wan...@ciac.jl.cn 2009-06-30 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parameters of Fe-S cluster
Hello Does anyone have the topology parameters for Fe-S cluster ? Subarna ICC World Twenty20 England #39;09 exclusively on YAHOO! CRICKET http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error
hey there, Can anyone of you pls help me rectify this error: Warning: 1-4 interaction between 903 and 912 at distance 374.354 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Can the Ifdef option be used in the rtp file?
Dear gmx users, According to the manual, Ifdef option can be used in the top file. One question comes to me as the letter title indicates since the top file can generate from the rtp file. Please give me the answer? Sincerely, Chaofu Wu _ Messenger10年嘉年华，礼品大奖等你拿！ http://10.msn.com.cn___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Can the Ifdef option be used in the rtp file?
wuxiao wrote: Dear gmx users, According to the manual, Ifdef option can be used in the top file. One question comes to me as the letter title indicates since the top file can generate from the rtp file. Please give me the answer? Yes. You can not use it. Sincerely, Chaofu Wu 立刻下载 MSN 保护盾，保障Messenger 安全稳定！ 现在就下载！ http://im.live.cn/safe/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology 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 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_potential calculation method
Dear Gromacs experts How can I find the theoritical method which is employed by Gromacs in order to caculate the electrostatic potential? Here is what is written in manual about g_potential: The potential is calculated by first summing the charges per slice and then integratingtwice of this charge distribution It's too vague! Thank you all -- Negar Ashari Astani ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Installation with non standard location of fftw3
Graham Kettlewell wrote: Hi Justin, I thought I might stop clogging the other people's inboxes, and mail you directly. It's better to keep things on the list. I don't necessarily have a final solution; maybe someone else will! I tried installing only the double precision version, and it failed the same way, so I tried doing the single precision, make distclean, and then the double precision. Exactly the same error: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library The contents of the lib directory now: -sh-3.2$ cd fftw/lib/ -sh-3.2$ ls -l total 4464 -rw-r--r-- 1 grahamk uowstf 2230376 Jun 30 15:28 libfftw3.a -rw-r--r-- 1 grahamk uowstf 2200524 Jun 30 15:24 libfftw3f.a -rwxr-xr-x 1 grahamk uowstf 956 Jun 30 15:24 libfftw3f.la -rw-r--r-- 1 grahamk uowstf 44862 Jun 30 15:24 libfftw3f_threads.a -rwxr-xr-x 1 grahamk uowstf 980 Jun 30 15:24 libfftw3f_threads.la -rwxr-xr-x 1 grahamk uowstf 953 Jun 30 15:28 libfftw3.la -rw-r--r-- 1 grahamk uowstf 44722 Jun 30 15:28 libfftw3_threads.a -rwxr-xr-x 1 grahamk uowstf 977 Jun 30 15:28 libfftw3_threads.la drwxr-xr-x 2 grahamk uowstf4096 Jun 30 15:28 pkgconfig -sh-3.2$ Indeed, now I am stuck. Your /lib directory contains what it should, as far as I can tell. Any warnings/errors from the compiler that would suggest something broke? There may also be some other useful diagnostic information in config.log. -Justin Thanks again, and sorry to be a pain. Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error
P.R.Anand Narayanan wrote: hey there, Can anyone of you pls help me rectify this error: Warning: 1-4 interaction between 903 and 912 at distance 374.354 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file See here: http://oldwiki.gromacs.org/index.php/blowing_up -Justin Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: SD temperature coupling groups
Hey!
I think Your problem is from function init_stochd in update.c
(src/mdlib).
When You set tau_t to 0 You got division by 0 on line 288:
for(n=0; nngtc; n++) {
sdc[n].gdt = ir-delta_t/ir-opts.tau_t[n];
sdc[n].eph = exp(sdc[n].gdt/2);
sdc[n].emh = exp(-sdc[n].gdt/2);
sdc[n].em = exp(-sdc[n].gdt);
I think the easiest solution, I checked it for sd1, is to change in
do_update_sd1 (update.c) following lines
for(d=0; dDIM; d++) {
if((ptype[n] != eptVSite) (ptype[n] != eptShell)
!nFreeze[gf][d]) {
sd_V = ism*sig[gt].V*gmx_rng_gaussian_table(gaussrand);
v[n][d] = v[n][d]*sdc[gt].em
+ (invmass[n]*f[n][d] + accel[ga][d])*tau_t[gt]*(1 -
sdc[gt].em)
+ sd_V;
xprime[n][d] = x[n][d] + v[n][d]*dt;
} else {
v[n][d] = 0.0;
xprime[n][d] = x[n][d];
}
}
to
for(d=0; dDIM; d++) {
if((ptype[n] != eptVSite) (ptype[n] != eptShell)
!nFreeze[gf][d] (tau_t[gt] != 0.0)) {
sd_V = ism*sig[gt].V*gmx_rng_gaussian_table(gaussrand);
v[n][d] = v[n][d]*sdc[gt].em
+ (invmass[n]*f[n][d] + accel[ga][d])*tau_t[gt]*(1 -
sdc[gt].em)
+ sd_V;
xprime[n][d] = x[n][d] + v[n][d]*dt;
} else {
if((ptype[n] != eptVSite) (ptype[n] != eptShell)
!nFreeze[gf][d]){
v[n][d] = v[n][d] + (invmass[n]*f[n][d] +
accel[ga][d])*dt;
xprime[n][d] = x[n][d] + v[n][d]*dt ;
}
else {
v[n][d] = 0;
xprime[n][d] = x[n][d]; }
}
}
You can do similar change for sd2.
Hope somebody corrects me if I am wrong.
Greetings
Andrzej
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] merge two PDBs
Hi everyone, can one still search the mailing list entries? I can't find it in the new site! A question: what would one want to do if he had a PDB file of a dimer and pdb2gmx couldn't analyse both of them, ending up giving some errors. I tried to separate two mers and then pdb2gmx'ed them getting nice topologies of each. But how can I merge them together again? the numbering will be messy. There should be some more human way for that :-) Editconf does not take two files and I don't want to put the other one at a random position since it needs to be just beside the other mer! What should one do at all, if one gets a NMR- based PDB which has the structure of more than one chemically equal species and wants to work with it? With Herzian thanks... Cheers, Peyman -- Peyman Yamin Institut fuer Strukturbiologie und Biophysik (ISB) ISB-3: Strukturbiochemie Forschungszentrum Juelich D-52425 Juelich Tel:(49)-2461-61-2875 Fax:(49)-2461-61-2023 mailto: p.yamin[at]fz-juelich.de Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] merge two PDBs
Peyman Yamin wrote: Hi everyone, can one still search the mailing list entries? I can't find it in the new site! I've posted this several times in the last few days: http://oldwww.gromacs.org/swish-e/search/search2.php A question: what would one want to do if he had a PDB file of a dimer and pdb2gmx couldn't analyse both of them, ending up giving some errors. I tried to separate two mers and then pdb2gmx'ed them getting nice topologies of each. But how can I merge them together again? the numbering will be messy. There should be some more human way for that :-) Editconf does not take two files and I don't want to put the other one at a random position since it needs to be just beside the other mer! What should one do at all, if one gets a NMR- based PDB which has the structure of more than one chemically equal species and wants to work with it? Concatenate the files using standard *nix utilities like cat, remove any repeated/unnecessary box information or REMARK lines, and use genconf to renumber. -Justin With Herzian thanks... Cheers, Peyman -- Peyman Yamin Institut fuer Strukturbiologie und Biophysik (ISB) ISB-3: Strukturbiochemie Forschungszentrum Juelich D-52425 Juelich Tel:(49)-2461-61-2875 Fax:(49)-2461-61-2023 mailto: p.yamin[at]fz-juelich.de Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] merge two PDBs
Hi, What error(s) do you get? /Erik Peyman Yamin skrev: Hi everyone, can one still search the mailing list entries? I can't find it in the new site! A question: what would one want to do if he had a PDB file of a dimer and pdb2gmx couldn't analyse both of them, ending up giving some errors. I tried to separate two mers and then pdb2gmx'ed them getting nice topologies of each. But how can I merge them together again? the numbering will be messy. There should be some more human way for that :-) Editconf does not take two files and I don't want to put the other one at a random position since it needs to be just beside the other mer! What should one do at all, if one gets a NMR- based PDB which has the structure of more than one chemically equal species and wants to work with it? With Herzian thanks... Cheers, Peyman -- Peyman Yamin Institut fuer Strukturbiologie und Biophysik (ISB) ISB-3: Strukturbiochemie Forschungszentrum Juelich D-52425 Juelich Tel:(49)-2461-61-2875 Fax:(49)-2461-61-2023 mailto: p.yamin[at]fz-juelich.de Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] few doubts regarding 1-4 interaction
Hi gromacs users, I am facing the same error during Production run that faced by so many gromacs users and I know this query has been answered for several times. But Could you please tell me some specific doubt regarding the 1-4 interaction error that usually occurs? I have equilibrated my protein ligand system of around 600 ps and shown a satisfied level of equilibration. Then I moved to the Production run of 3ns. But shows the same 1-4 interaction error. My doubts are, 1. It was advised by gromacs experts that better I should go for another round of minimization. Is it on the equilibrated structure? 2. If so Do i need to equilibrate again after minimization? 3. I have did 2500 steps of minimization on the structure which is equilibrated and then again run for 3ns production run But occured the same error at 3 lakh step? if I reduce my time step how that will affect this error(I have seen in the error section of gromacs that another possibility is to reduce the time step?) Can you please tell me your suggestion on these?? Thank you. Aswathy Dept. Biotechnology Ext. 3108 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Chlorophyll force field parameters
Dear all, I'm trying to evaluate the stability of a (bacterio)-chlorophyll docked into my protein active site, but it appears that there is no parameter for this molecule in gromacs force fields and PRODRG does not support Mg atoms. Does anyone have such parameters ? Cheers. -- MAUPETIT Julien - Plateforme RPBS MTi - Unite Inserm / Paris 7 Diderot U973 Université Paris Diderot Paris 7 Bâtiment Lamarck, 5ème étage unité MTI 36, rue Hélène Brion 75013 Paris FRANCE tel: +33 1 57 27 83 95 http://julien.maupetit.free.fr ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] few doubts regarding 1-4 interaction
Ms. Aswathy S wrote: Hi gromacs users, I am facing the same error during Production run that faced by so many gromacs users and I know this query has been answered for several times. But Could you please tell me some specific doubt regarding the 1-4 interaction error that usually occurs? I have equilibrated my protein ligand system of around 600 ps and shown a satisfied level of equilibration. Then I moved to the Production run of 3ns. But shows the same 1-4 interaction error. My doubts are, 1. It was advised by gromacs experts that better I should go for another round of minimization. Is it on the equilibrated structure? It would be good if you could remind us of what you are doing, as well as cite the actual post where you were told to do this. 2. If so Do i need to equilibrate again after minimization? Yes. 3. I have did 2500 steps of minimization on the structure which is equilibrated and then again run for 3ns production run But occured the same error at 3 lakh step? if I reduce my time step how that will affect this error(I have seen in the error section of gromacs that another possibility is to reduce the time step?) Reducing the timestep can in some cases finesse the problem into behaving. If there is something more deeply wrong with your model, then this probably won't help out a whole lot. If you can post a more complete description of what it is you are doing, what parameters you are using, etc. you might get more detailed suggestions. The bottom line is, if your system is blowing up, something about the model physics is unreasonable. -Justin Can you please tell me your suggestion on these?? Thank you. Aswathy Dept. Biotechnology Ext. 3108 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Chlorophyll force field parameters
I looked at one point. The only MD paper using Chlorophyll I found was Spezia et al Biophys J. 2003, 84:2805-13 On Jun 30, 2009, at 4:49 PM, Julien Maupetit wrote: Dear all, I'm trying to evaluate the stability of a (bacterio)-chlorophyll docked into my protein active site, but it appears that there is no parameter for this molecule in gromacs force fields and PRODRG does not support Mg atoms. Does anyone have such parameters ? Cheers. -- MAUPETIT Julien - Plateforme RPBS MTi - Unite Inserm / Paris 7 Diderot U973 Université Paris Diderot Paris 7 Bâtiment Lamarck, 5ème étage unité MTI 36, rue Hélène Brion 75013 Paris FRANCE tel: +33 1 57 27 83 95 http://julien.maupetit.free.fr ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Table Functions
Hi- I am trying to add an extra repulsive potential for neighboring hydroxyl groups on a carbon chain and have heard that this can be done using table functions. Is there a good resource on how to create these table function files or even someplace where I could get an example of them? Thanks. _ Windows Live™: Keep your life in sync. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_BR_life_in_synch_062009___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Charge pertubation
Hi all, There are a gromacs's program for introducing a charge value in residue or make modifications in the topology file?? How analises the residue's charge of a protein? Thank you Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulation of protein in presence of ATP
Hi nikhil damle When running pdb2bmx for ATP in a PDB file using the ffG43a1, shows warnings because atom names don't match. You have to cut the ATP coordinates out to other PDB file, to convert it to gromacs format (.gro) using editconf and edit this file in gromacs format to match the atom namings in the rtp file. Then, one can run pdb2gmx to that file in gromacs format to generate the topology for the ATP. When you have gotten this topology file, you can change its extension to ITP. By other side you need to run pdb2gmx for the rest of the molecule. Then you can merge the .gro files and the topology files, as explained in the GROMACS Tutorial for Drug-Enzyme Complex (http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf). Lucio PhD. Student Lab. Dr. Federico Sanchez Instituto de Biotecnologia, UNAM Mexico El lun, 22-06-2009 a las 10:09 +0530, nikhil damle escribió: Hi all, I want to carry out a MD simulation of a receptor protein in presence of ATP molecule. ATP is included in .rtp file of ffG43a1 force field. but post pdb2gmx, .pdb output file does not show crds of ATP. Does it mean that ATP is not recognized as a residue of protein in spite of being included in .rtp file. If so how does one carry out this simulation ? If .itp file of ATP is an option, how can one get the specific values of charges etc for constructing .itp file. Manual does not mention anything regarding it. Please help as soon as possible. Regards, Nikhil __ Love Cricket? Check out live scores, photos, video highlights and more. Click here. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_tune_pme in Ranger
Hi, I wonder whether somebody has been able to install g_tune_pme in Ranger (one of the tacc clusters). If so, please contact me off list as I have a couple of questions to ask. Patricia. -- Dr. Patricia Soto patricia.sot...@gmail.com ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 62, Issue 158
I am trying to add an extra repulsive potential for neighboring hydroxyl groups on a carbon chain and have heard that this can be done using table functions. Is there a good resource on how to create these table function files or even someplace where I could get an example of them? Thanks. The examples are in the topology folder of the gromacs installation. As for me they are quite self-explanatory. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to avoid generating wrong dihedrals?
Dear gmx users, I try to generate gro and top files using pdb2gmx, and this procedure finishs without any error. However, when I run grompp from these files, many errors are encountered such as: .. ERROR 124 [file g04.top, line 20027] No default Ryckaert-Bell. types .. I gusess it is dihedrals that cause these errors. So I look for the line 20027 in the file g04.top. only to find that these dihedrals are C-N-H-H, obviously wrong. How to avoid these errors? Could you give me some help to cope with them? Thank you for attention. Sincerely, Chaofu Wu _ 打工，挣钱，买房子，快来MClub一起”金屋藏娇”！ http://club.msn.cn/?from=10___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installation problem:fftw3f lib. not found.
Hi, I installed fftw as follows (creating single- and double-precision versions) : ./configure --enable-threads --enable-float --prefix=/home/kudesias/fftw make make install make distclean ./configure --enable-threads --prefix=/home/kudesias/fftw make make install I also used export CPPFLAGS=-I/home/kudesias/fftw/include export LDFLAGS=-L/home/kudesias/fftw/lib ( Initially I used I in place of L so I corrected it) On using the configure script ./configure --enable-mpi I get the following error then checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... 1 checking for sqrt in -lm... yes checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). I will be glad if you can help with this. Thanks On Thu, Jun 25, 2009 at 2:08 AM, Florian Dommert domm...@icp.uni-stuttgart.de wrote: * Shobhit Kudesia shobhit.kude...@gmail.com [2009-06-25 01:55:00 +0530]: Hi , During the ./configure of gromacs on my Bash Shell, I get the following error: configure: error: Cannot find fftw3f library I have installed fftw3 files in a directory other than usr/local. I have installed fftw3 both with double and single precision but I still get the error while configuration of GROMACS for default single precision. I have also included the libraries usinG CPPFLAGS LDFLAGS. If you have installed the single version of FFTW3 and supply the corresponding CPPFLAGS and LDFLAGS to configure then the script will find the libraries. So two errors are very likely though we do not anything about your installation: * a small typo in the configure line ( if you present it here, everybody can judge this ) * the installation of the single precision fftw3f failed for any reasons Flo Any help will be appreciated ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommerthttp://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert !! PGP-ENCODED emails preferred !! ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- With Warm Regards Shobhit Kudesia 3rd year Undergraduate Department of Biotechnology IIT Kharagpur ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] few doubts regarding 1-4 interaction
Thanks Justin. I am trying to do the simulation of protein-ligand complex. 1. Minimized the protein(but converged before the Fmax reached the threshold) 2. Did a 50 steps of NVT equilibration 3. Then an NPT equilibration reached at 650 steps (checked the RMSD with the initial structure) 4. Then tried to do a 3 ns production run. But failed ~ after 170 ps. I am attching the NPT file I have used for equilibration. Also the structure after equilibration does not have any clashes or bad contact in the rough analysis. How can I do a more close checking of this? Once again Thank you for your response. Aswathy - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, June 30, 2009 8:33:19 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] few doubts regarding 1-4 interaction Ms. Aswathy S wrote: Hi gromacs users, I am facing the same error during Production run that faced by so many gromacs users and I know this query has been answered for several times. But Could you please tell me some specific doubt regarding the 1-4 interaction error that usually occurs? I have equilibrated my protein ligand system of around 600 ps and shown a satisfied level of equilibration. Then I moved to the Production run of 3ns. But shows the same 1-4 interaction error. My doubts are, 1. It was advised by gromacs experts that better I should go for another round of minimization. Is it on the equilibrated structure? It would be good if you could remind us of what you are doing, as well as cite the actual post where you were told to do this. 2. If so Do i need to equilibrate again after minimization? Yes. 3. I have did 2500 steps of minimization on the structure which is equilibrated and then again run for 3ns production run But occured the same error at 3 lakh step? if I reduce my time step how that will affect this error(I have seen in the error section of gromacs that another possibility is to reduce the time step?) Reducing the timestep can in some cases finesse the problem into behaving. If there is something more deeply wrong with your model, then this probably won't help out a whole lot. If you can post a more complete description of what it is you are doing, what parameters you are using, etc. you might get more detailed suggestions. The bottom line is, if your system is blowing up, something about the model physics is unreasonable. -Justin Can you please tell me your suggestion on these?? Thank you. Aswathy Dept. Biotechnology Ext. 3108 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php md_NPT.mdp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] few doubts regarding 1-4 interaction
Ms. Aswathy S wrote: Thanks Justin. I am trying to do the simulation of protein-ligand complex. 1. Minimized the protein(but converged before the Fmax reached the threshold) What was the target Fmax? What Fmax did the EM converge to? 2. Did a 50 steps of NVT equilibration 50 steps? That is far too short to be effective. 3. Then an NPT equilibration reached at 650 steps (checked the RMSD with the initial structure) The NPT script you attached called for 5 steps. Did NPT stop prematurely? When applying position restraints, RMSD is meaningless as far as whether or not equilibration is effective. 4. Then tried to do a 3 ns production run. But failed ~ after 170 ps. I am attching the NPT file I have used for equilibration. Also the structure after equilibration does not have any clashes or bad contact in the rough analysis. How can I do a more close checking of this? You are using Shake to constrain bond lengths. LINCS is more stable. -Justin Once again Thank you for your response. Aswathy - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, June 30, 2009 8:33:19 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] few doubts regarding 1-4 interaction Ms. Aswathy S wrote: Hi gromacs users, I am facing the same error during Production run that faced by so many gromacs users and I know this query has been answered for several times. But Could you please tell me some specific doubt regarding the 1-4 interaction error that usually occurs? I have equilibrated my protein ligand system of around 600 ps and shown a satisfied level of equilibration. Then I moved to the Production run of 3ns. But shows the same 1-4 interaction error. My doubts are, 1. It was advised by gromacs experts that better I should go for another round of minimization. Is it on the equilibrated structure? It would be good if you could remind us of what you are doing, as well as cite the actual post where you were told to do this. 2. If so Do i need to equilibrate again after minimization? Yes. 3. I have did 2500 steps of minimization on the structure which is equilibrated and then again run for 3ns production run But occured the same error at 3 lakh step? if I reduce my time step how that will affect this error(I have seen in the error section of gromacs that another possibility is to reduce the time step?) Reducing the timestep can in some cases finesse the problem into behaving. If there is something more deeply wrong with your model, then this probably won't help out a whole lot. If you can post a more complete description of what it is you are doing, what parameters you are using, etc. you might get more detailed suggestions. The bottom line is, if your system is blowing up, something about the model physics is unreasonable. -Justin Can you please tell me your suggestion on these?? Thank you. Aswathy Dept. Biotechnology Ext. 3108 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hi all, Thanks a lot for the help extended to me through gmx-users' archives. Regards, Nikhil Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
