Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
Hi Berk, I tried this fix, but mdrun_mpi is still hanging. I'll try to use the debugger by the end of the week and let you know. Cheers, Patrick Berk Hess a écrit : Hi, My guess is that this is not the problem. But it is very easy to try, so please do. The diff for src/gmxlib/pbc.c is: 392c392,393 try[d] == 0; --- try[d] = 0; pos[d] = 0; Berk Date: Tue, 6 Jan 2009 18:37:20 +0100 From: patrick.fu...@univ-paris-diderot.fr To: gmx-users@gromacs.org Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Hi, I also fixed a problem with unitialized variables for pbc calculations in trilinic boxes. But up till now I have not observed any effect of this bug. Is your box triclinic? Yes it is. So shall I test your corrected version ? Patrick Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] minimization problems
Hongyan Xiao wrote: Hi, gmx-users, I built a system,decane(42molecule)/water(903)/decane(42), including the two decane/water interfaces. However, when I minimized this system, I found the system turn into water/decane(84)/water. That is to say in the initial system two parts of decane turn into a part, while water turns into two parts. I am surprised by the minimized result. Can you tell me the possible reasons? Thank you very much! Periodic boundary conditions? H. Y. Xiao ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] eigenvalues
On Thu, 8 Jan 2009 16:31:01 +0530 (IST) sanja...@iitb.ac.in wrote: dear gromacs users, i did PCA analysis for my trajectory using g_covar and g_anaeig, i have taken trajectory of 25ns from both protein alone and protein_withligands(i did two simulation one with ligands and other by removing the ligands from pdb file)and extracted eigenvalues along first 10 eigenvector, when i compared eigenvalues i find that protein_withligands has high values in compare to protein alone, but from literature protein alone is more flexible structure and after ligand binding it changes in to more rigid structure. primary analysis like RMSD, RMSF calculation showing high values for protein alone in compare to protien_withligands. i think i should also get higher eigenvalue for protein alone.. is any thing wrong with my trajectory. i had used same mdp file for both simulation. i am sending values of Ist 10 eigenvector for make my question more clear. any suggestion is appreciable The eigenvalues alone do not mean much. They probably do not correspond to the same eigenvectors. You have to compare the eigenvectors from the two simulations. This is possible using a RMSIP (root mean square inner product). You'll find the definition and more details in papers from Amadei and Ceruso. hints: Amadei et al., 1999; Ceruso et al., 1999a,b, 2003; Merlino et al., 2003; Roccatano et al., 2003 Best, XAvier. protein-withligands 1 1.48497 2 0.674994 3 0.410547 4 0.279636 5 0.237182 6 0.213209 7 0.158359 8 0.140052 9 0.126227 10 0.113618 protein alone 1 0.526848 2 0.351471 3 0.267247 4 0.248945 5 0.222829 6 0.204475 7 0.158441 8 0.12583 9 0.0970591 10 0.0923962 thanks sanjay ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] minimization problem
Hongyan Xiao wrote: Hi, David van der Spoel I used the periodic boundary conditions. The box is 3.006x3.002x6.000 along x,y,z direction,respectively.The following is the em.mdp file. Then the minimization works correctly. See chapter 3 in the manual. ; ; User xiao ; 2008.9.28 10:23 ; Input file ; cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 2 nstcomm = 1 ns_type = grid rlist = 0.8 coulombtype = cut-off rcoulomb= 1.2 vdwtype = cut-off rvdw= 1.2 Tcoupl = no Pcoupl = no gen_vel = no Please help me. Thanks again! H. Y. Xiao ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Forces are large - How to track down the culprit
Hi Shay, sorry for the late comment - let me guess, you compiled Gromacs in double precision? :) Greetings Steffen Is this reproducible? Yes. I've taken the same simulation and had it re-run and got the same error at the exact same frame (frame 693, which is timeframe 6930). You could try to fork off a tpr file using tpbconv -f -e -s -o just before this happens and rerun it. I did something similar to what you suggest before posting here: Oddly enough the Warning did not occur: I ran the simulation up to 6000ps and then continued the simulation to another 4000ps and the simulation ran correctly and without any problems. It can also be combined by input parameters, e.g. too large time step, too infrequent neighborsearching etc., use of cutoffs. If no other suggestions I'll try working that angle too, since a lot of my simulations are running with very similar mdp parameters without problems. Thanks again for your prompt reply, -Shay Shay Amram wrote: Of course. I'm using version 3.3.3 of GROMACS. -Shay -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Tuesday, December 30, 2008 02:59 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Forces are large - How to track down the culprit Shay Amram wrote: Greetings dear Gromacs users, I have recently been simulating a POPG membrane* in water (SPC). Several of my simulations after running well into the 10ns and 20ns are sometimes getting a Forces for atom X are large. I'm rather unsure as to the cause of this situation. Moreover, as far as I can tell from viewing the simulation, the system _does NOT_ explode (as may be suggested by wiki.gromacs and some previous answers to this kind of situation). The rest of the simulation looks much as it did in the beginning. I would be interested (and thankful!) to hear any of your opinions as to why I'm getting this message (or how to catch the culprit), and more importantly, how to prevent it from happening in the future. During this version-transitive period, it's always right to report the GROMACS version that you're using. It would normally be right to be using the most recent version (4.0.2) if encountering problems. 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 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School 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: sw...@bph.rub.de Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] minimization problem
Hi, I has used the periodic boundary conditions and correct em.mdp file. However, the minimized result is water/decane/water, while I set decane/water/decane as the initial system . I cannot understand the reason. Please give me some constructive suggestion! Thanks! H. Y. Xiao ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] minimization problem
Hongyan Xiao wrote: Hi, I has used the periodic boundary conditions and correct em.mdp file. However, the minimized result is water/decane/water, while I set decane/water/decane as the initial system . I cannot understand the reason. Please give me some constructive suggestion! Thanks! Your system is probably not centered in the box, and thus PBC is reconstructing it. Use ngmx to see how Gromacs is viewing your system. -Justin H. Y. Xiao ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] minimization problem
Hongyan Xiao wrote: Hi, I has used the periodic boundary conditions and correct em.mdp file. However, the minimized result is water/decane/water, while I set decane/water/decane as the initial system . I cannot understand the reason. Please give me some constructive suggestion! Thanks! You need to understand that decane/water/decane under periodic boundary conditions has only one interface... the two decane segments are contiguous. Further, there's nothing magical about where you've placed that interface with respect to your initial box, since there are an infinite number of mathematically equivalent alternatives. The physics of the system and the algorithms in GROMACS will feel free to ignore your arbitrary choice. If you want to reconstruct a particular choice after a simulation, you will need to play around with editconf and/or trjconv. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with running mdrun in parallel
Hi there, I am trying to run an MD simulation on a 13 residue peptide with distance restraints. Before, I ran into a problem with this system when an error message occurred during mdrun concerning distance restraints and domain decomposition. There was apparently a bug in mshift.c and the bug was fixed. However, at this point, my simulation works properly only if I use the serial version of mdrun. When I try to run it in parallel, I get this error message: NNODES=4, MYRANK=0, HOSTNAME=chong06.chem.pitt.edu NNODES=4, MYRANK=2, HOSTNAME=chong06.chem.pitt.edu NNODES=4, MYRANK=3, HOSTNAME=chong06.chem.pitt.edu NNODES=4, MYRANK=1, HOSTNAME=chong06.chem.pitt.edu NODEID=0 argc=13 NODEID=3 argc=13 NODEID=2 argc=13 NODEID=1 argc=13 :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.0.2 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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. :-) /home/map110/gromacs.4.0.2patched/bin/mdrunmpi (-: Option Filename Type Description -s md.tpr InputRun input file: tpr tpb tpa -o md.trr Output Full precision trajectory: trr trj cpt -x md.xtc Output, Opt! Compressed trajectory (portable xdr format) -cpi state.cpt Input, Opt. Checkpoint file -cpo state.cpt Output, Opt. Checkpoint file -c md.gro Output Structure file: gro g96 pdb -e md.edr Output Energy file: edr ene -g md.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file -fieldfield.xvg Output, Opt. xvgr/xmgr file -tabletable.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -tableb table.xvg Input, Opt. xvgr/xmgr file -rerunrerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpitpi.xvg Output, Opt. xvgr/xmgr file -tpid tpidist.xvg Output, Opt. xvgr/xmgr file -eisam.edi Input, Opt. ED sampling input -eosam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jobam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -px pullx.xvg Output, Opt. xvgr/xmgr file -pf pullf.xvg Output, Opt. xvgr/xmgr file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -deffnm string Set the default filename for all file options -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -[no]sum bool yes Sum the energies at every step -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 15 Checkpoint interval (minutes) -[no]append bool no Append to previous output files when restarting from checkpoint -maxhreal -1 Terminate after 0.99 times this
[gmx-users] unit of the opls-aa force field in Gromacs package
Hello Could someone tell me what are the exact units of the force constants of bond and angle term of the OPLS-aa force field implemented in the Gromacs package? Thank you in advance Sunjoo ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] unit of the opls-aa force field in Gromacs package
sunny...@gmail.com wrote: Hello Could someone tell me what are the exact units of the force constants of bond and angle term of the OPLS-aa force field implemented in the Gromacs package? Table 5.4 in the manual. -Justin Thank you in advance Sunjoo ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Onw question about rlist rvdw rcoulomb and nstlist
Dear all gromacs users: Usually when we do neighbour searching we should give three parameters: cut-off distance, buffer length and the frequency of the neighbour list updating. But in Gromacs *.mdp file it's just required to give rlist,nstlist, rvdw and rcoumlomb. Where is the buffer length of neighbour searching in Gromacs? Best wishes! xuji x...@home.ipe.ac.cn 2009-01-09 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Onw question about rlist rvdw rcoulomb and nstlist
xuji wrote: Dear all gromacs users: Usually when we do neighbour searching we should give three parameters: cut-off distance, buffer length and the frequency of the neighbour list updating. But in Gromacs *.mdp file it's just required to give rlist,nstlist, rvdw and rcoumlomb. Where is the buffer length of neighbour searching in Gromacs? If I understand your question correctly, you are inferring the need for a user-supplied buffer length from the usual practice in some other MD code. GROMACS uses dynamic memory allocation for constructing the neighbour lists, so there is no reason for the user to provide an arbitrary size, like one might have done in the days of FORTRAN77. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
