Re: [gmx-users] DNA orientation restrain
On Monday 01,October,2012 01:44 PM, 仝督读 wrote: Hi everyone, I am doing a DNA simulation in a long simulation box (the lengthen of z is much larger than x and y). So I want to constrain the DNA molecule lying along the z axis. But I don't know how to realize this in GROMACS. Actually I notice there is orientation restraints in 4.3.5 of GMX Manual. But the orientation value is set to be observables of NMR experiments, such as this example: ; ai aj type exp. label alpha const. obs. weight 31 32 1 1 3 3 6.083 -6.73 1.0 But how can I set the observable in my case as it's not an NMR experiment? Any suggestion will be appreciate. Thanks very much Dudu, notice the posre.itp? ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 change the fz value to be high enough, like below: 1 1 1000 1000 5 this 5 I just made up here as example, you may try to pick a reasonable one. Dudu Tong 31%2032%201%201%203%203 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that segmentation fault Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_tcaf segmentation fault
On Thursday 27,September,2012 12:55 AM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? -f traj.trr InputFull precision trajectory: trr trj cpt Here the full precision means double precision? I see you use single precision. I have never tried this one, perhaps someone else may give you some suggestions. Best regards, Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that segmentation fault Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. Ο χρήστης lina lina.lastn...@gmail.com έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Protein ligand molecular dynamics simulation
On Mon, Apr 16, 2012 at 11:01 PM, sai nitin sainit...@gmail.com wrote: Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology which is in complex structure. Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool (http://swissparam.ch/) when i do Editconf and created cubic box ligand is going away from protein. Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics. Can any body tell me how to do this..? 1] pdb2gmx generate ligands.top (if possible, basically you need generate your ligand.itp by other ways) and rename it as ligands.itp 2] pdb2gmx generate protein.top and rename it as protein.itp (also need delete some entry) 3] create the topol.top includes the ligands.itp and protein.itp, take care the double entry. (To make it easy, you may take some pdb with several chains. use pdb2gmx and see how those top files combined together.) 4] The docked structure skip the pdb2gmx step. go directly to the editconf. You may do a try, but it will be helpful if you are a bit familiar with how to combine those top_files. Thanks in advance -- Sainitin D -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to change the timestamp of a xtc file
Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to change the timestamp of a xtc file
On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai p...@uab.edu wrote: trjcat -settime or trjconv -t0 Thank you, a further question, a trjcat-ed xtc file, which timestamp like 0-5 0-2 0-5 0-3 ... Are there someway to update them all in the trjcated ones? Thanks ahead, On 2012-04-05 03:59:44PM +0800, lina wrote: Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] which xtc file should be used for the trjconv command
On Thu, Apr 5, 2012 at 11:50 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, In the on-line tutorial on lysozyme (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html), there is a command trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact Will you please consider in that command whether we can change md_1_1.xtc to state.xtc? Yes. I am looking forward to getting your reply. Cheers, Acoot -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] something about tpr file
Hi, suppose I lost original .tpr file, can I get tpr file from the .xtc file ? I mean from the .xtc or trr file, not by re-run grompp to generate tpr file. Thanks ahead, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to change the timestamp of a xtc file
On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 05/04/12, lina lina.lastn...@gmail.com wrote: On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai p...@uab.edu wrote: trjcat -settime or trjconv -t0 Thank you, a further question, a trjcat-ed xtc file, which timestamp like 0-5 0-2 0-5 0-3 ... Are there someway to update them all in the trjcated ones? I've no idea what you mean, but trjconv -settime is still your friend. sorry I didn't say it clearly. Well, I mean several xtc files all starts with 0 but ends with 1 ns, 2 ns, 1 ns I use trjcat -cat combine them together. now I wonder can make the time continuously. from 0 to 4ns. Thanks, Mark Thanks ahead, On 2012-04-05 03:59:44PM +0800, lina wrote: Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] the different protonation state of HIS
On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, For the different protonation state of HIS, what are there 3-letter code for GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me to read? Do we still have any other confusing amino acids? In pdb2gmx -his you will get something like below 0. H on ND1 only (HSD) 1. H on NE2 only (HSE) 2. H on ND1 and NE2 (HSP) 3. Coupled to Heme (HIS1) Then based on the pka value and the PH, you can make a choice. I am looking forward to getting a reply from you. Cheers, Acoot -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] em fatal error!
On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila oina...@gmail.com wrote: We are trying to do simulation of lysozyme in water. step with problem : energy minimization. command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 4.0.5 (-: 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. :-) grompp (-: Option Filename Type Description -f minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 1AKI_solv_ions.gro Input Structure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p topol.top Input Topology file -pp processed.top Output, Opt. Topology file -o em.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.0.5 You use Version 4.0.5. If I remember correctly, the earlier version has different pname. (seems one is NA+, one is NA) If I were you, I would update to latest version and try. Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype NA what should we do -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] continue replica exchange MD
On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas a.ku...@herts.ac.uk wrote:
Hello,
Upon continuing a replica exchange MD simulation using the command
mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 1
-cpt 60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e
edrRemd_20ns.edr -stepout 2000
From my side, I have no problem resuming or extending the REMD
simulations in V.4.5.5 and 4.5.4
Here is the command:
mdrun_g_f -s md_.tpr -multi 32 -replex 500 -cpi state_.cpt -append
I use state_.cpt, not state.cpt
I get the following output:
**
...
...
500 steps, 1.0 ps (continuing from step 49430, 98.9 ps).
500 steps, 1.0 ps (continuing from step 49430, 98.9 ps).
step 49430, will finish Wed Sep 12 16:09:33 2012
step 5, will finish Thu May 24 11:23:04 2012
Step 47546: resetting all time and cycle counters
= PBS: job killed: walltime 604823 exceeded limit 604800
Terminated
**
Apparently, the job runs for one week on a computer cluster (that is the
maximum time allowed), but it does not progress very much beyond step 49430.
Also the log-file does not show any more steps:
Step Time Lambda
46455 92.91000 0.0
Grid: 18 x 17 x 25 cells
Energies (kJ/mol)
G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
5.83095e+04 3.70277e+04 2.14102e+03 8.83853e+03 -7.33070e+02
Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
2.29503e+05 3.04138e+05 -2.66781e+04 -8.51221e+03 -2.74692e+06
Coul. recip. Position Rest. Potential Kinetic En. Total Energy
-9.59421e+05 5.41532e+03 -3.09689e+06 5.18959e+05 -2.57793e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.97550e+02 -1.14933e+02 5.41944e+01 0.0e+00
Writing checkpoint, step 49430 at Fri Jan 27 09:43:23 2012
---
Restarting from checkpoint, appending to previous log file.
...
...
Started mdrun on node 0 Tue Mar 6 16:40:10 2012
Step Time Lambda
49430 98.86000 0.0
Grid: 18 x 17 x 25 cells
Energies (kJ/mol)
G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
5.84241e+04 3.69121e+04 2.09533e+03 8.80916e+03 -4.67086e+02
Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
2.29528e+05 2.99825e+05 -2.67028e+04 -8.51334e+03 -2.74410e+06
Coul. recip. Position Rest. Potential Kinetic En. Total Energy
-9.59506e+05 5.47116e+03 -3.09823e+06 5.18993e+05 -2.57923e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.97570e+02 -1.14963e+02 2.67842e+00 0.0e+00
Step Time Lambda
5 100.0 0.0
Energies (kJ/mol)
G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
5.86161e+04 3.71585e+04 2.15336e+03 8.92946e+03 -4.84684e+02
Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)
2.29950e+05 3.01014e+05 -2.66724e+04 -8.51306e+03 -2.74349e+06
Coul. recip. Position Rest. Potential Kinetic En. Total Energy
-9.59537e+05 5.56712e+03 -3.09531e+06 5.19371e+05 -2.57594e+06
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.97787e+02 -1.14956e+02 2.36460e+01 1.50068e-05
[End of log-file]
***
I wonder, if this is my mistake (using the mdrun wrongly), a Gromacs problem
or maybe a problem of the computer cluster (MPI, etc). I would be grateful
for any help.
Many thanks
Andreas--
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Re: [gmx-users] Generating topology
On Thu, Mar 22, 2012 at 11:54 AM, Spring buds winterho...@gmail.com wrote: Hi A protein sits on the top of another protein (not docking). I then used pdb2gmx command to generate the topology. Surprisingly, i got five files, as given below: I think the two proteins are not connected each other. is it possible to make it one posre and topol file. You have already have one posre and topol.top more topol.top check what's inside your topol.top. pay attention to include Many thanks in advance posre_Protein_chain_A.itp posre_Protein_chain_A2.itp topol.top topol_Protein_chain_A.itp topol_Protein_chain_A2.itp -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist without output file
On Sat, Mar 10, 2012 at 7:14 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear all When I use g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5, program was done without error, but it don't create output file (dist.xvg) in the directory in which g_dist tool was run. What is reason of this case? Try without the -dist 0.5, you will get the -o dist.xvg output. the -dist is Print all atoms in group 2 closer than dist to the center of mass of group 1 Any help will highly appreciated. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist without output file
On Sat, Mar 10, 2012 at 9:17 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Lina Thanks for your reply. Without the -dist 0.5, I get the -o dist.xvg output, but I need list of the all atoms in group 2 closer than dist to the center of mass of group 1. It print on the terminal, you may notice it. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist without output file
On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Lina There is not any things related to list of atoms on the terminal. t: 100 83 ILE 845 CG1 1.60274 (nm) t: 100 83 ILE 846 CG2 1.63838 (nm) t: 100 83 ILE 847 CD 1.59769 (nm) t: 100 83 ILE 848 C 1.8202 (nm) t: 100 83 ILE 849 O 1.86972 (nm) t: 100 84 ALA 850 N 1.88309 (nm) t: 100 84 ALA 851 H 1.85958 (nm) t: 100 84 ALA 853 CB 1.99705 (nm) Last frame 50 time 100.000 gcq#310: Shoot them the atom now (The Ramones) g_dist_g -f try_1.xtc -s try_1.tpr -dt 5 -b 0 -e 100 -dist 2 -n index_1.ndx Best regards -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist without output file
On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Lina There is not any things related to list of atoms on the terminal. Might your distance -dist so large. try a smaller one and see. Best regards -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] dssp and gromacs version
On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 2/03/2012 6:52 PM, lina wrote: Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, The new DSSP is not compatible with any GROMACS Ha ... the dssp complain the segmentation fault in 4.5.5, but can run smoothly in 4.5.3. IIRC, seems there were some threads talked about that before. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] dssp and gromacs version
Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PBC - Protein and Ligands
On 1 Mar, 2012, at 1:01, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The problem I face is PBC which I cannot get rid of. I used: 1. First make your molecules whole if you want them whole (system). trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame (system) trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc So the trajecory of my ligands is smooth but they do do bind to the different periodic images. As i know it is impossible to obtain the proper trajectory of all of them I just want to obtain the realistic final positions of my system to extract pdb file for further umbrella sampling. Any suggestions? You may wanna try Trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -ur compact -o pdbs.pdb -dt 1000 Please change dt if necessary. Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Implicit solvent - Gromacs 4.5.4
On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann s.neuman...@gmail.com wrote: Thank you Vedat! Why do you use -DFLEXIBLE in md and in em? Why dont you use constraint algorithm (LINCS) in your simulation? Otherwise, the system is easily explode with lots of LINCS warning. Also thanks Vedat for sharing, Best regards, Steven On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz dur...@zib.de wrote: hi steven, i've been simulating a 33 AA peptide for the past two days using implicent solvent in order to achieve a proper folding. i haven't added counterions, however, the systems shows nice results according to what i've expected. the mdrun command (for the extension) for our hardware looks as follows: mpiexec -np 4 mdrun -pd -s md.tpr -append -cpi md.cpt -deffnm md 21 and here's the mdp file for the energy minimization: define = -DFLEXIBLE constraints = none integrator = steep dt = 0.001 ; ps nsteps = 3 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb = 0 rvdw = 0 comm-mode = angular comm-grps = Protein optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 5.0 emstep = 0.01 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = Still ; HCT ; OBC nstgbradii = 1 rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = -1 and for the md run: define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 10 ; 10 ps = 100 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb = 0 rvdw = 0 comm-mode = angular comm-grps = system optimize_fft = yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 300 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp = 300 gen_seed = -1 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = Still ; HCT ; OBC nstgbradii = 1 rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = -1 best regards, vedat Am 28.02.2012 11:59, schrieb Steven Neumann: Dear Gmx Users, I am using Gromacs 4.5.4 and I would like to implement implicit solvent for folding of my protein. I read mailing list and it is still confusing for me. Is it proper to use counterions within the system? If not, how can I obtain netral system? Do we use cut off for vdw and coulombic interactions? What kind of integrator should be used with a timestep? I will appreciate an mdp file for protein folding! Thank you Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
[gmx-users] how to extract the x y z
Hi, I don't know how to extract the position like the x y z with t or r with t. Thanks for any suggestions, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Problem with simulation of Protein-DNA complex
On Thu, Feb 9, 2012 at 8:44 PM, rar...@ens-cachan.fr wrote: Dear Gromacs users, I have been trying to simulate a Protein-DNA complex using gromacs, but each time I have been facing problems. I would like to point out that both the Protein and DNA have been modeled and after that docked in order to obtain a complex. Following are the parameters I am using: Force-Field: amber99sb-ildn water model: TIP3P 40 NA ions were added in order to neutralise the complex-solvent system. Gromacs doesn't show any error up until I proceed to do nvt equilibriation. Before the NVT, you may do some energy minimization. Following is nvt.mdp: title = PFV_DNA_NVT define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 100 ; 2 * 5 = 100 ps dt = 0.001 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracyi ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed It generates a tpr, but upon mpirun gives the following error: starting mdrun 'Protein in water' 100 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.027514, max 0.979682 (between atoms 3460 and 3461) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3455 3457 65.2 0.1542 0.2535 0.1526 3455 3456 33.3 0.1093 0.1322 0.1090 3457 3459 72.7 0.1105 0.1739 0.1090 3457 3458 65.7 0.1105 0.1588 0.1090 3460 3469 78.6 0.1409 0.2693 0.1400 3460 3461 78.8 0.1409 0.2772 0.1400 3461 3463 75.1 0.1406 0.1489 0.1400 3463 3465 37.2 0.1403 0.1756 0.1400 3463 3464 40.7 0.1083 0.1408 0.1080 3465 3467 35.5 0.1403 0.1733 0.1400 3467 3469 74.0 0.1405 0.1373 0.1400 3467 3468 42.9 0.1083 0.1433 0.1080 Wrote pdb files with previous and current coordinates Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 364940.065742, max 11977066.00 (between atoms 3465 and 3466) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3475 3495 110.8 0.1526 20544.7148 0.1522 3475 3477 111.6 0.1529 20544.4336 0.1526 3475 3476 108.1 0.1094 20543.1309 0.1090 3477 3480 62.8 0.1527 4.6441 0.1526 3477 3479 57.5 0.1091 4.5683 0.1090 3477 3478 93.6 0.1091 4.6160 0.1090 3495 3497 138.1 0.1336 4.9133 0.1335 3495 3496 69.6 0.1230 4.9085 0.1229 3497 3499 40.2 0.1449 0.2036 0.1449 3497 3498 43.8 0.1010 0.1527 0.1010 3480 3483 35.6 0.1526 0.1902 0.1526 3480 3482 42.2 0.1090 0.1501 0.1090 3480 3481 41.7 0.1090 0.1485 0.1090 3453 3455 88.7 0.1701 117322.3672 0.1449 3453 3454 88.3 0.1035 65066.2227 0.1010 3455 3471 48.9
Re: [gmx-users] how to get the block averaged MSD curve ?
On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim ilmare...@gmail.com wrote: Hi, I have a simulation result from 0 to 50ns after equilibration run. I want to divide this data set equally into 10blocks (10ns each) and get block averaged MSD curve (average of 10 blocks). I would try some external software. excel. It seems that I mange to get block MSD data by using g_msd -beginfit 0 -endfit 10, g_msd -beginfit 10 -endfit 20, Then the output files are msd1.xvg, msd2.xvg,..,msd10.xvg (10 xvg files) My question is that how can I get averaged MSD from this outputs?? It seems that g_analyze is appropriate to do this. g_analyze -n 10 -av ?? Could anybody tell me how to get averaged MSD using g_analyze (each block data has different x values but same length) ? Another question is that what is the difference bwn g_msd and g_analyze -msd ?? Is there any reference of posting to obtain this information ? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Error energy minimization on protein with implicit water
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr The minim.mdp file = ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 emtol = 1.0 kJ/mol nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple ; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = no ; Periodic Boundary Conditions (yes/no) I get a note as = System has non-zero total charge: -4.96e+00 then i tried using genion step as= genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log then again the grompp step and mdrun . but while doing mdrun i get an error as= Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 but here i have given nsteps as 5000 so why does it stop. -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv select group
On Friday 03,February,2012 09:56 PM, francesca vitalini wrote: Yes but those tips are not for bash scripts... :( You'd better post what you have done so far about this script, probably someone can help you improve or refine it. 2012/2/3 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 4/02/2012 12:21 AM, francesca vitalini wrote: Hi! I have to use the gromacs command trjconv to obtain a .gro file from a .xtc and a .pdb file. I have to do it for several files in a bash for loop so I'd rather prefer to find a way to make my script type in the trjconv interactive terminal always the same number for the system. Any tips? Check out http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv select group
On Friday 03,February,2012 10:02 PM, francesca vitalini wrote:
Sure!
My code is
#!/bin/bash
for ((i=1; i=357; i=$i+3))
do
trjconv -f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o
../cg_gro/300-${i}.gro -pbc whole
try touch a file as index.txt and put 0 in the index.txt
trjconv -f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o
../cg_gro/300-${i}.gro -pbc index.txt
done
very stupidly I just need to type 0 all the time in the interactive
window that trjconv opens.
Any help?
Thanks
2012/2/3 lina lina.lastn...@gmail.com mailto:lina.lastn...@gmail.com
On Friday 03,February,2012 09:56 PM, francesca vitalini wrote:
Yes but those tips are not for bash scripts... :(
You'd better post what you have done so far about this script,
probably someone can help you improve or refine it.
2012/2/3 Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.__au mailto:mark.abra...@anu.edu.au
On 4/02/2012 12:21 AM, francesca vitalini wrote:
Hi!
I have to use the gromacs command trjconv to obtain a
.gro file
from a .xtc and a .pdb file. I have to do it for several
files
in a bash for loop so I'd rather prefer to find a way to
make my
script type in the trjconv interactive terminal always
the same
number for the system. Any tips?
Check out
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts
http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
Mark
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Re: [gmx-users] reg. error
On Fri, Feb 3, 2012 at 12:54 PM, Vishwambhar Bhandare vishway...@gmail.com wrote: Hello, I am getting error given below, wht we can do for this? Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2gmx.c, line: 655 Fatal error: Atom 'H5T in residue A 1 was not found in rtp entry RA5 with 31 atoms while sorting atoms. Pay attention to check the residue A 1 in your input .gro file, and then check the .rtp file in the some_path_to/share/gromacs/top/_your_choice_of_force_field/rtp file. . Thanks and Regards, -- Vishwambhar Centre for Bioinformatics Pondicherry University Pondicherry -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Minimization Problems
On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling selin...@msu.edu wrote: Hello, I've recently been having trouble with my simulations blowing up. Specifically, This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size for a few interactions, with each of them approaching inf. Can anyone find anything glaringly wrong with my .mdp? Thanks, Alex Seling title = Minimization of alpha-synuclein cpp = /lib/cpp -traditional define = -DFLEXIBLE integrator = sd constraints = none tinit = 0 dt = 0.001 nsteps = 100 emtol = 0.1 emstep = 0.1 nstcgsteep = 1000 bd-fric = 0 nstlog = 50 nstenergy = 1 gen_temp = 273 gb_epsilon_solvent = 78.3 implicit_solvent = GBSA gb_algorithm = Still nstcomm = 10 xtc_precision = 1000 gen_vel = yes nstxtcout = 0 nstxout = 100 pbc = no energygrps = system nstfout = 0 nstvout = 0 niter = 20 nstlist = 10 it's more about your .gro file (system), less about the .mdp file. -- gmx-users mailing list gmx-userstheromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Trajectory
On Mon, Jan 30, 2012 at 5:43 PM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I run the simulation of protein with 10 ligands (200 ns). In total I should have total of 4000 frames as I set up: nsteps = 1 dt = 0.002 nstxout = 25000 I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump -dt 4000 now you will only have 51 frames. more info. check trjconv -h The trajectory which I read in VMD has 3008 frames and my ligands completely disappear after 8 frame (They are not in PBC windows which I checked in Graphics - Graphical Representation - Periodic) Can you please advise? I think I have to many frames in my trajectory, how can I reduce it in trjconv? Thank you, Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] simulation killed
did you write this script yourself? On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik mehmet63...@hotmail.com wrote: hi! lina my script this please tell me where is wrong...thanks #!/bin/bash # Set some environment variables FREE_ENERGY=/home/mkiytak/Free_Energy1 echo Free energy home directory set to $FREE_ENERGY MDP=$FREE_ENERGY/MDP echo .mdp files are stored in $MDP LAMBDA=0 # A new directory will be created for each value of lambda and # at each step in the workflow for maximum organization. Here add: if [ -d Lambda_$LAMBDA ]; then rm -r Lambda_$LAMBDA fi mkdir Lambda_$LAMBDA cd Lambda_$LAMBDA # # ENERGY MINIMIZATION 1: STEEP # # echo Starting minimization for lambda = $LAMBDA... mkdir EM_1 cd EM_1 # Iterative calls to grompp and mdrun to run the simulations grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro -p $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm min$LAMBDA # # ENERGY MINIMIZATION 2: L-BFGS # # cd ../ mkdir EM_2 cd EM_2 grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3 # Run L-BFGS in serial (cannot be run in parallel) mdrun -nt 1 -deffnm min$LAMBDA echo Minimization complete. # # NVT EQUILIBRATION # # echo Starting constant volume equilibration... cd ../ mkdir NVT cd NVT grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3 One thing, do you use define = -DPOSRES in your nvt_0.mdp, if yes, you need take care where your posre.itp file stored. mdrun -nt 8 -deffnm nvt$LAMBDA echo Constant volume equilibration complete. # # NPT EQUILIBRATION # # echo Starting constant pressure equilibration... cd ../ mkdir NPT cd NPT grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p Here $ LAMBDA -- $LAMBDA, no space. $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm npt$LAMBDA echo Constant pressure equilibration complete. # # PRODUCTION MD # # echo Starting production MD simulation... cd ../ mkdir Production_MD cd Production_MD grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm md$LAMBDA echo Production MD complete. # End echo Ending. Job completed for lambda = $LAMBDA Date: Mon, 30 Jan 2012 13:54:18 +0800 Subject: Re: [gmx-users] simulation killed From: lina.lastn...@gmail.com To: gmx-users@gromacs.org On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik mehmet63900@hotm ail.com wrote: hi again capacity of my harddisk 600 GB ı try again ..the program gave me below message... Reading file md0.tpr, VERSION 4.5.4 (single precision) Starting 8 threads NOTE: The load imbalance in PME FFT and solve is 1211%. For optimal PME load balancing PME grid_x (1152) and grid_y (1152) should be divisible by #PME_nodes_x (8) and PME grid_y (1152) and grid_z (1152) should be divisible by #PME_nodes_y (1) Making 1D domain decomposition 8 x 1 x 1 starting mdrun 'Protein in water' 250 steps, 5000.0 ps. ./job_0.sh: line 95: 15777 Killed mdrun -nt 8 -deffnm What's inside your job_0.sh? something wrong your script. md$LAMBDA Production MD complete. Ending. Job completed for lambda = 0 mkiytak@babil:~/JOB1$ How can I solve this problemthanks for your help. Date: Sun, 29 Jan 2012 10:43:53 -0600 From: p...@uab.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] simulation killed something killed your job but it wasn't gromacs. Your system has run time or memory requirements that your job exceeded. On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote: hi! all ı have to a big problem..ı am doing free energy calculation for a ligand (L histidine ) when ı perform mdrun .. my simulation stop ... the program gave me this message.. Reading file md0.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Making 1D domain decomposition 8 x 1 x 1 gt; starting mdrun 'Protein in water' 250 steps, 5000.0 ps. ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm md$LAMBDA Production MD complete. Ending. Job completed for lambda = 0 mkiytak@babil:~/JOB1$ my mdp file.. gt ; ; Run control integrator = sd ; Langevin dynamics tinit = 0 dt = 0.002 nsteps = 250 ; 5 ns nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0
Re: [gmx-users] simulation killed
On Mon, Jan 30, 2012 at 9:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: did you write this script yourself? This script appears to be based on one that I provided in the free energy tutorial, but there are some differences (including one of the mistakes you Your tutorials were well-written. I read some of them. but not this one. so ... note below). It would be helpful if the OP explained what these simulations were doing, as well as if they are attempting the tutorial or some other different system. -Justin On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik mehmet63...@hotmail.com wrote: hi! lina my script this please tell me where is wrong...thanks #!/bin/bash # Set some environment variables FREE_ENERGY=/home/mkiytak/Free_Energy1 echo Free energy home directory set to $FREE_ENERGY MDP=$FREE_ENERGY/MDP echo .mdp files are stored in $MDP LAMBDA=0 # A new directory will be created for each value of lambda and # at each step in the workflow for maximum organization. Here add: if [ -d Lambda_$LAMBDA ]; then rm -r Lambda_$LAMBDA fi mkdir Lambda_$LAMBDA cd Lambda_$LAMBDA # # ENERGY MINIMIZATION 1: STEEP # # echo Starting minimization for lambda = $LAMBDA... mkdir EM_1 cd EM_1 # Iterative calls to grompp and mdrun to run the simulations grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro -p $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm min$LAMBDA # # ENERGY MINIMIZATION 2: L-BFGS # # cd ../ mkdir EM_2 cd EM_2 grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3 # Run L-BFGS in serial (cannot be run in parallel) mdrun -nt 1 -deffnm min$LAMBDA echo Minimization complete. # # NVT EQUILIBRATION # # echo Starting constant volume equilibration... cd ../ mkdir NVT cd NVT grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3 One thing, do you use define = -DPOSRES in your nvt_0.mdp, if yes, you need take care where your posre.itp file stored. mdrun -nt 8 -deffnm nvt$LAMBDA echo Constant volume equilibration complete. # # NPT EQUILIBRATION # # echo Starting constant pressure equilibration... cd ../ mkdir NPT cd NPT grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p Here $ LAMBDA -- $LAMBDA, no space. $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm npt$LAMBDA echo Constant pressure equilibration complete. # # PRODUCTION MD # # echo Starting production MD simulation... cd ../ mkdir Production_MD cd Production_MD grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr -maxwarn 3 mdrun -nt 8 -deffnm md$LAMBDA echo Production MD complete. # End echo Ending. Job completed for lambda = $LAMBDA Date: Mon, 30 Jan 2012 13:54:18 +0800 Subject: Re: [gmx-users] simulation killed From: lina.lastn...@gmail.com To: gmx-users@gromacs.org On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik mehmet63900@hotm ail.com wrote: hi again capacity of my harddisk 600 GB ı try again ..the program gave me below message... Reading file md0.tpr, VERSION 4.5.4 (single precision) Starting 8 threads NOTE: The load imbalance in PME FFT and solve is 1211%. For optimal PME load balancing PME grid_x (1152) and grid_y (1152) should be divisible by #PME_nodes_x (8) and PME grid_y (1152) and grid_z (1152) should be divisible by #PME_nodes_y (1) Making 1D domain decomposition 8 x 1 x 1 starting mdrun 'Protein in water' 250 steps, 5000.0 ps. ./job_0.sh: line 95: 15777 Killed mdrun -nt 8 -deffnm What's inside your job_0.sh? something wrong your script. md$LAMBDA Production MD complete. Ending. Job completed for lambda = 0 mkiytak@babil:~/JOB1$ How can I solve this problemthanks for your help. Date: Sun, 29 Jan 2012 10:43:53 -0600 From: p...@uab.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] simulation killed something killed your job but it wasn't gromacs. Your system has run time or memory requirements that your job exceeded. On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote: hi! all ı have to a big problem..ı am doing free energy calculation for a ligand (L histidine ) when ı perform mdrun .. my simulation stop ... the program gave me this message.. Reading file md0.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Making 1D domain decomposition 8 x 1 x 1 gt; starting
Re: [gmx-users] simulation killed
On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik mehmet63...@hotmail.com wrote: hi again capacity of my harddisk 600 GB ı try again ..the program gave me below message... Reading file md0.tpr, VERSION 4.5.4 (single precision) Starting 8 threads NOTE: The load imbalance in PME FFT and solve is 1211%. For optimal PME load balancing PME grid_x (1152) and grid_y (1152) should be divisible by #PME_nodes_x (8) and PME grid_y (1152) and grid_z (1152) should be divisible by #PME_nodes_y (1) Making 1D domain decomposition 8 x 1 x 1 starting mdrun 'Protein in water' 250 steps, 5000.0 ps. ./job_0.sh: line 95: 15777 Killed mdrun -nt 8 -deffnm What's inside your job_0.sh? something wrong your script. md$LAMBDA Production MD complete. Ending. Job completed for lambda = 0 mkiytak@babil:~/JOB1$ How can I solve this problemthanks for your help. Date: Sun, 29 Jan 2012 10:43:53 -0600 From: p...@uab.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] simulation killed something killed your job but it wasn't gromacs. Your system has run time or memory requirements that your job exceeded. On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote: hi! all ı have to a big problem..ı am doing free energy calculation for a ligand (L histidine ) when ı perform mdrun .. my simulation stop ... the program gave me this message.. Reading file md0.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Making 1D domain decomposition 8 x 1 x 1 gt; starting mdrun 'Protein in water' 250 steps, 5000.0 ps. ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm md$LAMBDA Production MD complete. Ending. Job completed for lambda = 0 mkiytak@babil:~/JOB1$ my mdp file.. ; Run control integrator = sd ; Langevin dynamics tinit = 0 dt = 0.002 nsteps = 250 ; 5 ns nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 0 xtc-precision = 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no g t; ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t = 1.0 ref_t = 300 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-05 ref_p = 1.0 ; Free energy control stuff free_energy = yes init_lambda = 0.00 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-moltype = system couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = non e ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 PLEASE HELP ME... WHY THE PROGRAM STOP ( KİLLED) SORRY FOR BAD ENGLİSH.. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)s ubscribe 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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe
Re: [gmx-users] umbrella-drug
On Sat, Jan 28, 2012 at 9:17 PM, parto haghighi parto.haghi...@gmail.com wrote: Dear gmx-users I am working on lipid membrane+drug system.I should do umbrella sampling in this procedure: 1.cat drug and lipid 2.energy minimization 3.run npt 4.run md_pull I want to pull drug into the membrane but gromacs pushes the drug to the sides of box.and this result is independent of drug location Also I have used 500 ps for my simulation time but when I use ngmx to see the process,it runs only 56 ps.why? What can I do when I want to move drug to the bilayer? You may want to check the pull_vec1 and pull_k -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] adding hydrogen
Hi, are there some tips of quick adding missing atoms ( namely hydrogens, non-titrable ones, or some ligands ones) ? Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] force field
Hi, which gromacs force field shares the high quasi-compatibility with the amber force field. I checked the heme only exists in gromos and the charmn while gbsa only shows in amber and oplsaa, truth is that I don't know how to get the gbsa parameter for heme, Thanks for any suggestions, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Implicit solvent model in Gromacs
On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Dear gromacs users list, I noticed that gromacs can perform simulations with an implicit solvent model using a GBSA method. Is it compatible with the CHARMM22 force field? look for gbsa.itp showed amber03.ff/forcefield.itp amber03.ff/gbsa.itp amber94.ff/forcefield.itp amber94.ff/gbsa.itp amber96.ff/forcefield.itp amber96.ff/gbsa.itp amber99.ff/forcefield.itp amber99.ff/gbsa.itp amber99sb.ff/forcefield.itp amber99sb.ff/gbsa.itp amber99sb-ildn.ff/forcefield.itp amber99sb-ildn.ff/gbsa.itp amberGS.ff/forcefield.itp amberGS.ff/gbsa.itp oplsaa.ff/forcefield.itp oplsaa.ff/gbsa.itp seems not. Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Postdoc at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] About g_rms and the XPM file format
On Mon, Jan 23, 2012 at 9:56 PM, Víctor victor.gil.sepulv...@gmail.com wrote: Dear all, I've been trying to do a rmsd matrix of two different trajectories by using g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm g_rms uses does something like this: for each frame f1 in traj1: for each frame f2 in traj2: superimpose f1 , f2 calculateRMSD f1, f2 Or like this (as I've seen in some other rmsd matrix calculation scripts): for each frame f in traj1: superimpose f with first frame for each frame f1 in traj1: for each frame f2 in traj2: calculateRMSD f1, f2 I've also been trying to convert the resulting xpm file to a readable file BTW, xpm file is readable. try: more xpm or other tools your preferred to read. in order to process it using python. Is there any tool to do this kind of conversion?(Btw I've been trying to find this kind of tool with not much luck). There's enough info on the file to be able to parse it easily, but using a 3rd party tested tool would be more convenient. Thanks! -- Víctor Gil Sepúlveda E. Informatica - FIB - UPC -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Implicit solvent model in Gromacs
On Tue, Jan 24, 2012 at 12:08 AM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Dear gromacs users list, I noticed that gromacs can perform simulations with an implicit solvent model using a GBSA method. Is it compatible with the CHARMM22 force field? look for gbsa.itp showed amber03.ff/forcefield.itp amber03.ff/gbsa.itp amber94.ff/forcefield.itp amber94.ff/gbsa.itp amber96.ff/forcefield.itp amber96.ff/gbsa.itp amber99.ff/forcefield.itp amber99.ff/gbsa.itp amber99sb.ff/forcefield.itp amber99sb.ff/gbsa.itp amber99sb-ildn.ff/forcefield.itp amber99sb-ildn.ff/gbsa.itp amberGS.ff/forcefield.itp amberGS.ff/gbsa.itp oplsaa.ff/forcefield.itp oplsaa.ff/gbsa.itp seems not. It's called gb.itp in the charmm27.ff subdirectory. Thanks. your information is very helpful. I know the answer asked on another thread. -Justin Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Postdoc at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Installing uninstalling of gromacs
On 24 Jan, 2012, at 1:53, Spring buds winterho...@gmail.com wrote: Dear Gromacs users, Greetings!!! I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for past four days. But still I am not able to. So I would like to ask some questions which are below. 1.My laptop is a dual core, which means two processors?.So should I need to install MPI? --enable threads 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used the which gromacs and it shows as /usr/bin/which: no mdrun in (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin). However, I used rm -rf /usr/local/gromacs to remove installing I still can see tha gromacs files with red background in /usr/local/bin. Could you tell me I removed the gromacs installing? You have not. 3.Could you please tell me the very simple steps for installatios, since I am a novice. http://www.gromacs.org/Downloads/Installation_Instructions Many thanks in advance for your time and help. Huang Malai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Installing uninstalling of gromacs
On Tue, Jan 24, 2012 at 11:42 AM, Spring buds winterho...@gmail.com wrote: Hi lina, Thanks for reply. could you tell me how to remove completly the gromacs installation? Which commands have you issued? try make uninstall in the directory where you used make install before. like Path_to//gromacs-4.5.5 and then make distclean for a totally clear re-installation, removed the /gromac-4.5.5 and re-untar the gromacs-4.5.5.tar.gz before that, further check the lib and bin have totally removed or not. Which OS you are working on? On Tue, Jan 24, 2012 at 2:31 AM, lina lina.lastn...@gmail.com wrote: On 24 Jan, 2012, at 1:53, Spring buds winterho...@gmail.com wrote: Dear Gromacs users, Greetings!!! I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for past four days. But still I am not able to. So I would like to ask some questions which are below. 1.My laptop is a dual core, which means two processors?.So should I need to install MPI? --enable threads 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used the which gromacs and it shows as /usr/bin/which: no mdrun in (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin). However, I used rm -rf /usr/local/gromacs to remove installing I still can see tha gromacs files with red background in /usr/local/bin. Could you tell me I removed the gromacs installing? You have not. 3.Could you please tell me the very simple steps for installatios, since I am a novice. http://www.gromacs.org/Downloads/Installation_Instructions Many thanks in advance for your time and help. Huang Malai -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Failed to lock: md.log. No locks available.
Hi, Failed to lock: md.log. No locks available. still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Failed to lock: md.log. No locks available.
On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system, and not with GROMACS. Possibly some phantom process still thinks it owns the file. It's something relevant to the server. I am not experienced to figure it out even did some rough try. will drop an email to administrator. Thanks, Mark still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Failed to lock: md.log. No locks available.
On Fri, Jan 13, 2012 at 7:04 PM, Jianguo Li ljg...@yahoo.com.sg wrote: There is a solution in this mailing list sometime before: mv md.log to some other folder and copy it back. Jianguo I tried, not work. Thanks, From: lina lina.lastn...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 13 January 2012, 18:51 Subject: Re: [gmx-users] Failed to lock: md.log. No locks available. On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system, and not with GROMACS. Possibly some phantom process still thinks it owns the file. It's something relevant to the server. I am not experienced to figure it out even did some rough try. will drop an email to administrator. Thanks, Mark still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] unscribe
On Thursday 12,January,2012 09:36 AM, yp sun wrote: Dear Sir, I want to unscribe there emails, thank. http://lists.gromacs.org/mailman/listinfo/gmx-users at the bottom, fill in your email address and click Unsubscribe. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- *12年1月12日，周四, Mark Abraham /mark.abra...@anu.edu.au/* 写道： 发件人: Mark Abraham mark.abra...@anu.edu.au 主题: Re: [gmx-users] REMD error 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年1月12日,周四,上午9:28 On 12/01/2012 11:54 AM, bharat gupta wrote: Hi, I am trying to run a REMD of a peptide. But while executing the following command after nvt and npt equilibration , I am getting the following error:- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000 mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot enable executable stack as shared object requires: Permission denied You configured GROMACS to use shared libraries, but something about them or your current environment doesn't work. Try rebuilding GROMACS, building with static libraries, or discussing with your system admins. Mark -- gmx-users mailing list gmx-users@gromacs.org http://cn.mc156.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 http://cn.mc156.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] REMD error
On Thursday 12,January,2012 08:54 AM, bharat gupta wrote: Hi, I am trying to run a REMD of a peptide. But while executing the following command after nvt and npt equilibration , I am getting the following error:- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000 mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot enable executable stack as shared object requires: Permission denied Can you run a normal md smoothly? try: mdrun_mpi mdrun -deffnm prefix_0 if it works, then some of your trajectories not sound. means system does not equilibrium well. Can anybody suggest me how could I rectify this error. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] exploding system
Hi, I met a very untamed simulation system. when I tried to run a short MD, it's collapsed with LINCS Warnings, It's under 317K so I used energy minimizations after NVT, and run another NVT_2 again. (In vacuum, no NPT being applied here). after that NVT_2, mainly increased the steps, run MD, it's collapsed again after 500ps, so I used the energy minimization from that nvt_2.gro several times, and it's collapsed during energy minimizations. Might I used wrong way of handling it. I tried 300K, which can run a bit further without collapse. Thanks for any suggestions you may give. Do I need to work hard on the energy minimization or? Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] which may caused this error
Hi, I have very high frequency meeting below error: [hostname-c06:07555] *** Process received signal *** [hostname-c06:07555] Signal: Segmentation fault (11) [hostname-c06:07555] Signal code: Address not mapped (1) [hostname-c06:07555] Failing at address: 0x2aaab3248120 [hostname-c06:07555] [ 0] /lib64/libpthread.so.0 [0x399440e7c0] [hostname-c06:07555] [ 1] /home/lina/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x1cc1) [0x2b7249a92d61] [hostname-c06:07555] [ 2] /home/lina/lib/libgmx_mpi.so.6(do_nonbonded+0xe8) [0x2b72499d99d8] [hostname-c06:07555] [ 3] /home/lina/lib/libmd_mpi.so.6(do_force_lowlevel+0x32f) [0x2b724931c7bf] [hostname-c06:07555] [ 4] /home/lina/lib/libmd_mpi.so.6(do_force+0xbf5) [0x2b72493766c5] [hostname-c06:07555] [ 5] mdrun_g_f(do_md+0x54ba) [0x41b1ca] [hostname-c06:07555] [ 6] mdrun_g_f(mdrunner+0x1169) [0x415ae9] [hostname-c06:07555] [ 7] mdrun_g_f(main+0x9c7) [0x41c027] [hostname-c06:07555] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3993c1d994] [hostname-c06:07555] [ 9] mdrun_g_f(do_cg+0x191) [0x407e39] [hostname-c06:07555] *** End of error message *** -- mpirun noticed that process rank 52 with PID 7555 on node hostname-c06 exited on signal 11 (Segmentation fault). I have made a clear installation with 4.5.5. just please feel free to give some wild guess about what's the possible reasons, Thanks with best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Implicit solvent tutorial
On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni gianluca.sant...@ibs.fr wrote: Hi gmx_users, is there any tutorial for implicit solvent simulation available? Hi, I tried it few days ago. 1] pdb2gmx the water model choose none. 2] after editconf, go to energy minimization directly * It's important to relax the system well. 3] NVT 4] You may find one .mdp file from gromacs-gpubench-dhfr.tar.gz At bottom also attached the one I tried. If some part is wrong, please let me know. Thanks, define = -DPOSRES integrator = sd nsteps = 10 dt = 0.0005 nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 continuation= yes constraints = all-bonds ns_type = grid nstlist = 1.0 rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 coulombtype = Cut-off pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = A B C tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 pbc = xyz gen_vel = no ld_seed = -1 implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii = 1.0 gb_epsilon_solvent = 80 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = 0.0054 Thanks! -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Implicit solvent tutorial
On Thu, Dec 8, 2011 at 11:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni gianluca.sant...@ibs.fr wrote: Hi gmx_users, is there any tutorial for implicit solvent simulation available? Hi, I tried it few days ago. 1] pdb2gmx the water model choose none. 2] after editconf, go to energy minimization directly * It's important to relax the system well. 3] NVT 4] You may find one .mdp file from gromacs-gpubench-dhfr.tar.gz At bottom also attached the one I tried. If some part is wrong, please let me know. You should not use PBC. Cutoffs should be infinite (i.e. all set to zero). Thanks, I noticed the example in the gromacs-gpubench-dhfr.tar.gz use PBC=no and Cut-off is infinite. I have never achieved stable simulations with finite cutoffs, even long ones, in implicit solvent simulations. Thanks for reminding. The tcoupl setting is ignored when using the sd integrator, and there is very little need to do any position restraining in implicit solvent simulations, as there is no solvent to relax, you're just restraining the protein and not accomplishing anything. gen_vel should be set to yes to generate velocities following EM. Thanks again, I restrained some peptides, another peptides are free. hopefully it will work. -Justin Thanks, define = -DPOSRES integrator = sd nsteps = 10 dt = 0.0005 nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 continuation = yes constraints = all-bonds ns_type = grid nstlist = 1.0 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 coulombtype = Cut-off pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = A B C tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 pbc = xyz gen_vel = no ld_seed = -1 implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii = 1.0 gb_epsilon_solvent = 80 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = 0.0054 Thanks! -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Convert xpm to matrix
On Sun, Dec 4, 2011 at 3:04 PM, Alex Jemulin alexbioi...@yahoo.com wrote: Dear all, I'd like to convert an xpm file to delimited CSV , because I need to import values in excel. Any suggestion? Try to write some scripts to do this. Thanks -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to understand this sentence
The Y-size of the box (1.999239) times the triclinic skew factor (1.00) is smaller than the number of DD cells (2) times the smallest allowed cell size (1.00) I don't understand the fatal error message it has been given during a simple run, I tested with large box already, during editconf I used -d 30 already, it's a very small peptide, the box dimension is 63.95000 60.76600 62.99900 Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: how to understand this sentence
https://docs.google.com/open?id=0B93SVRfpVVg3NTVjMmY0NzEtM2UzOC00MDEwLWI2OWMtZjEyZDQ5NzM1YWVh I uploaded the files here. is it the box still small? Thanks, On Thu, Dec 1, 2011 at 12:25 AM, lina lina.lastn...@gmail.com wrote: The Y-size of the box (1.999239) times the triclinic skew factor (1.00) is smaller than the number of DD cells (2) times the smallest allowed cell size (1.00) I don't understand the fatal error message it has been given during a simple run, I tested with large box already, during editconf I used -d 30 already, it's a very small peptide, the box dimension is 63.95000 60.76600 62.99900 Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to understand this sentence
On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 1/12/2011 3:25 AM, lina wrote: The Y-size of the box (1.999239) times the triclinic skew factor (1.00) is smaller than the number of DD cells (2) times the smallest allowed cell size (1.00) I don't understand the fatal error message it has been given during a simple run, I tested with large box already, during editconf I used -d 30 already, it's a very small peptide, the box dimension is 63.95000 60.76600 62.9990 Your system may be too small to parallelize over the number of processors you are using (and as usual, it would have been a good idea to supply your mdrun command line unless you enjoy wasting time when people make wrong guesses). As you can see it's a very small job, so I just run on laptop, now I changed the mdrun -nt 4 it showed: Fatal error: The X-size of the box (3.994507) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.00) The Fatal error about the Y-size when I used mdrun -nt 8 can you guess which is wrong here. on the last email the URL contains the md.mdp, topol.top and .gro files to run a mdrun. Thanks, Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to understand this sentence
Now I used mdrun -nt 2 it showed: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. and mdrun -nt 1 it showed: Program mdrun, VERSION 4.5.4-dev-20110711-dadcb Source code file: /var/local/cache/git-build/gromacs/src/gromacs/mdlib/ns.c, line: 2544 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. On Thu, Dec 1, 2011 at 11:38 AM, lina lina.lastn...@gmail.com wrote: On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 1/12/2011 3:25 AM, lina wrote: The Y-size of the box (1.999239) times the triclinic skew factor (1.00) is smaller than the number of DD cells (2) times the smallest allowed cell size (1.00) I don't understand the fatal error message it has been given during a simple run, I tested with large box already, during editconf I used -d 30 already, it's a very small peptide, the box dimension is 63.95000 60.76600 62.9990 Your system may be too small to parallelize over the number of processors you are using (and as usual, it would have been a good idea to supply your mdrun command line unless you enjoy wasting time when people make wrong guesses). As you can see it's a very small job, so I just run on laptop, now I changed the mdrun -nt 4 it showed: Fatal error: The X-size of the box (3.994507) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.00) The Fatal error about the Y-size when I used mdrun -nt 8 can you guess which is wrong here. on the last email the URL contains the md.mdp, topol.top and .gro files to run a mdrun. Thanks, Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] diffusion of the water at the micelle surface
On Sat, Nov 26, 2011 at 11:17 PM, chris.ne...@utoronto.ca wrote: When people do this for lipid bilayers, they compute depth-dependent diffusion profiles (often diffusion is computed separately for lateral diffusion and diffusion along the bilayer normal). Sounds like you might do something similar. I doubt that the standard gromacs tools will do this for you. If you don't hear from anybody about how to do this, then I'd suggest that you simply use g_dist to get the time-dependent distance for each water molecule and then use g_traj to output the coordinates of each water molecule and then script it yourself after reading one of the papers where people compute depth-dependent diffusion profiles for a lipid bilayer. Chris. -- original message -- I would like to compute the translational diffusion around the micelle surface. I know that I can select the water molecules at x distance of the micelle surface with g_select (right ?) but how to use this file generated by g_select to compute de diffusion, since the index and/or the number of water will change with the simulation time . You may try g_density, choose different time interval. Thank you for your response Stephane -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Adding ions using genion
On Thu, Nov 24, 2011 at 5:16 PM, cuong nguyen nvcuon...@gmail.com wrote: Dear, I create a box of water with 10 MIBC molecules on two opposite surfaces. then I used the command grompp -f input_min.mdp -o min.tpr -c box1.g96 to creat .tpr file before using the command genion -s min.tpr -o add.gro -nname Cl -pname NA -nn 20 -np 20 to add 20 Na+ and 20 Cl- into this box. I run the command grompp -f input_min.mdp -o min.tpr -c add.gro again and appeared the warings : Warning: atom name 176 in topol.top and add.gro does not match (CL - OW) Warning: atom name 177 in topol.top and add.gro does not match (CL - HW1) Warning: atom name 178 in topol.top and add.gro does not match (CL - HW2) Warning: atom name 179 in topol.top and add.gro does not match (CL - OW) Warning: atom name 180 in topol.top and add.gro does not match (CL - HW1) There is a mis-match between your .top file and .gro file. (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 72]: 21754 non-matching atom names atom names from topol.top will be used atom names from add.gro will be ignored .. Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. then I tried with the command grompp -f input_min.mdp -o min.tpr -c add.gro -maxwarn 2000 and it run well. However, when I kept working with the command mdrun -s min -o min -c min.g96 -x min -e min -g min, the errors appeared as follow: Fatal error: 3 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please help me to fix this problem. Many thanks. Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] No locks available.
On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz rol...@utk.edu wrote: Hi, Well, thanks, here comes the questions you asked before. what file system is this? What operating system on the compute node? In case it is a network file system what file system is used underneath and what operating system is the file server using? What version of GROMACS are you using? CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) 2.6.9-42.0.10.ELlargesmp #1 SMP Tue Feb 27 09:59:08 EST 2007 x86_64 x86_64 x86_64 GNU/Linux Gromacs, VERSION 4.5.3 If you need more information, please feel free to let me know. Best regards, As you workaround you should be able to run with mdrun -noappend. Roland On Sun, Nov 13, 2011 at 10:43 AM, lina lina.lastn...@gmail.com wrote: Hi, This is the first time I met: Fatal error: Failed to lock: md.log. No locks available the disk is not saturated, md.log is normal, The job was stopped months ago, and now I planned to resume it with all the necessary files kept intact. Thanks for pointing out which parts I should examine, Best regards, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Topology dihedral or improper dihedral
On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG yujan2...@gmail.com wrote: Hi there I am trying to build up a topology file for a tetra nitrogen molecule using Gromos UA and OPLS UA force field. Following are the molecules. 1. for C | A. C-C-C-C-C-C-C-N-C and | C C | B. C-C-C-C-C-C-C-N-C-C-C-C-COOH | C I have several questions: For A, the first molecule, should I use improper dihedral for the N-(CH3)3 or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any differences when using different force field (GROMOS and OPLS-UA)? For B, the second molecule, should I use improper dihedral for the N-(CH3)3 or proer dihedral for C-C-N-C with multi 2? Is there any differences when using different force field (GROMOS UA and OPLS UA)? The first expression about improper didedral is a planer restriction. When read the manual it also refers to the tetrahedral structure like this tetra nitrogen functional group. My question is when it has really long hydrocarbon tail, I guess it will be hard to flip over to the mirror images. Or it is not true in the simulation? You may take one built by other server, such as http://davapc1.bioch.dundee.ac.uk/prodrg/ as reference, and built yourself if necessary. Thank you very much!!! Best! Xueming -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] No locks available.
Hi, This is the first time I met: Fatal error: Failed to lock: md.log. No locks available the disk is not saturated, md.log is normal, The job was stopped months ago, and now I planned to resume it with all the necessary files kept intact. Thanks for pointing out which parts I should examine, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] No locks available.
On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz rol...@utk.edu wrote: Hi, what file system is this? What operating system on the compute node? In case it is a network file system what file system is used underneath and what operating system is the file server using? What version of GROMACS are you using? As you workaround you should be able to run with mdrun -noappend. Thanks, There is no problem running a mdrun without appending. Best regards, Roland On Sun, Nov 13, 2011 at 10:43 AM, lina lina.lastn...@gmail.com wrote: Hi, This is the first time I met: Fatal error: Failed to lock: md.log. No locks available the disk is not saturated, md.log is normal, The job was stopped months ago, and now I planned to resume it with all the necessary files kept intact. Thanks for pointing out which parts I should examine, Best regards, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] setting working directory
On Tue, Nov 1, 2011 at 3:33 PM, Efrat Exlrod efrat.exl...@biu.ac.il wrote:
Hi There!
Is it possible to run mdrun from a shared directory and set the working
directory to a local directory on the computer on which it runs, in order to
decrease NFS load?
Yes. I attached a generic script, you can modify from it if you want.
##project set up by the user
GENERICNAME=Your_project_name
## input data folder
INPUTDATAFOLDER=${HOME}/data
## cluster environment
shared scratch folder
SCRATCH=${HOME}/globalscracth
node local scratch folder
LOCALSCRATCH=${LOCALSCRATCH:-/scratch}/${USER}
## set up a unique tag suffix
JOBSUFFIX=$(date +%Y_%m_%d-%H_%M_%S-%N)-$$
## job name
JOBNAME=${GENERICNAME}-${JOBSUFFIX}
## share job working directory
JOBFOLDER=${SCRATCH}/${JOBNAME}
mkdir -p ${JOBFOLDER}
## local job working directory
LOCALJOBFOLDER=${LOCALSCRATCH}/${JOBNAME}
mkdir -p ${LOCALJOBFOLDER}
## let work on the local computer
cd ${LOCALJOBFOLDER}
## let transfert input data
cp -p ${INPUTDATAFOLDER}/*.data .
## let begin the job
## let transfert output data
mv outputdata.data ${JOBFOLDER}
## clean up the local scratch
cd ..
rm -rf ${JOBNAME}
## go home
cd
## exit
exit 0
##
## eos
Thanks, Efrat
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Re: [gmx-users] lost ngmx
On Sat, Oct 29, 2011 at 12:51 AM, Victor nicegrom...@live.cl wrote: Hello gmx-users I have compiled gromacs on Debian/Linux wiht the option --with-x but the ngmx binary has not been generated. I don´t have gnome or kde installed, but I have installed xserver-xorg and I can export VMD with ssh. Do I need to install gnome or kde? if the answer is yes, Do I need to compile gromacs again? or Is there a way to just compile ngmx? There is a .deb ball in the debian repository. http://packages.debian.org/sid/gromacs so you may try sudo aptitude install gromacs It will check the dependencies for you and install those dependent package (which also contains the GNOME staff in it). Thanks in advance -- Víctor E. Bahamonde Padilla Laboratorio Fisicoquimica Molecular Departamento de Química Facultad de Ciencias Universidad de Chile Phone: 562-978-7443 vedua...@ug.uchile.cl -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] problem with Threading during run
On Mon, Oct 31, 2011 at 9:28 AM, Sanku M msank...@yahoo.com wrote: Hi, I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to make use of threading introduced in gromacs 4.5.x series, it does not work. After issuing command like mdrun -v -s , I expected that for my 8-core processor which is not running any other jobs, the threading will show one job with 800 % cpu usage. But, it is showing 100 % cpu usage hence using only 1 of the 8 processors. I was wondering whether there is any command mdrun -t number_of_processors line I need to use to ensure the gromacs understands that there is 8 processors in a core and force make full use of the entire machine. I have tried the same thing in another different cluster where I found that threading works with showing 800 % cpu usage . But, for this cluster , the threading does not work. and make sure during your compile process, enable --threads Any help will be appreciated. Sanku -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 Tsjerk On Oct 28, 2011 6:27 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Make su... I used the initial mdrun .tpr. After checking the generated pdb (total 51 frames), the first 28/29 frames both are together, but later are separated. (the intra_fit also not work as expected). So I think at beginning the reference initial ones are together. This .xtc were trjcat together, first 200ns and then extend to 500ns, the .pdb generated used dt 10ns. Cheers, Am I wrong in some places? Actually for other trajectories I had no problem (use the same way of handling it). Thanks, Tsjerk On Oct 27, 2011 11:47 AM, lina lina.lastn...@gmail.com wrote: Hi, I have ... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists attachment: Screenshot-2.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, My previous reply was from before I looked at the graph. Have you considered that the molecule might be taking a stroll and turn back, Ha ... stroll?! or goes to another side of the protein? Have you looked at the trajectory, in particular at the trajectory with the jumps removed? I extracted the parts from 280ns to 300ns, the presentation of that part protein is not whole. In the former way, the time since 280ns till the end, the small molecular still outside the cell/box. even the minidist is very small later. I am not sure how to get the trajectory and view? (ngmx? ) Thanks, Cheers, Tsjerk On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Don't combine fitting, centering and pbc options. It may not work as expected. That's why the workflow is given. Use separate passes. By the way, first centering on the protein followed by putting molecules in the box should also work. Cheers, Tsjerk On Oct 28, 2011 9:01 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 Tsjerk On Oct 28, 2011 6:27 AM, lina lina.lastn...@gmail.com wrote: On Fri, Oct 28... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] trjconv and -pbc
Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, while this small molecular outside, I did not meet such issue before, it's used to be easy to fix the pbc problem, but not this one. a bit surprise, They are supposed to be together, Thanks for any advice, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan j.marzine...@imperial.ac.uk wrote: From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of lina [lina.lastn...@gmail.com] Sent: Thursday, October 27, 2011 10:47 AM To: Discussion list for GROMACS users Subject: [gmx-users] trjconv and -pbc Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, while this small molecular outside, I did not meet such issue before, it's used to be easy to fix the pbc problem, but not this one. a bit surprise, They are supposed to be together, Thanks for any advice, I am sure it will help. Follow the workflow! http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc Just use the trjconv -h to see each option. Ha, I think I have tried those options. That's why I am confused. Thanks, Jan === Jan Marzinek PhD Candidate Centre for Process Systems Engineering Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ E: j.marzine...@imperial.ac.uk M: +44(0)7411 640 552 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Fri, Oct 28, 2011 at 11:47 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/10/2011 2:39 PM, lina wrote: On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan j.marzine...@imperial.ac.uk wrote: From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of lina [lina.lastn...@gmail.com] Sent: Thursday, October 27, 2011 10:47 AM To: Discussion list for GROMACS users Subject: [gmx-users] trjconv and -pbc Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, while this small molecular outside, I did not meet such issue before, it's used to be easy to fix the pbc problem, but not this one. a bit surprise, They are supposed to be together, Thanks for any advice, I am sure it will help. Follow the workflow! http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc Just use the trjconv -h to see each option. Ha, I think I have tried those options. That's why I am confused. Thanks, Well, you need to try them better :) If you want your trajectory to keep protein and something else together, you will need an index group that combines them not jumping, and then combines them centering (or whatever). Thanks. I did use the index group on trjconv to output the pdb of the protein and the small molecular. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] trjconv and -pbc
On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Make sure to use a reference in which the molecules are together (clustered) the way you want them. I used the initial mdrun .tpr. After checking the generated pdb (total 51 frames), the first 28/29 frames both are together, but later are separated. (the intra_fit also not work as expected). So I think at beginning the reference initial ones are together. This .xtc were trjcat together, first 200ns and then extend to 500ns, the .pdb generated used dt 10ns. Cheers, Am I wrong in some places? Actually for other trajectories I had no problem (use the same way of handling it). Thanks, Tsjerk On Oct 27, 2011 11:47 AM, lina lina.lastn...@gmail.com wrote: Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, while this small molecular outside, I did not meet such issue before, it's used to be easy to fix the pbc problem, but not this one. a bit surprise, They are supposed to be together, Thanks for any advice, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Domain decomposition error in alchemical free energy perturbation MD
On Sat, Oct 15, 2011 at 2:11 PM, Xiaoxiao He xxia...@ust.hk wrote:
Dear all,
I'm doing an slow-growth alchemical free energy perturbation calculation
of the formation of a disulfide bridge between two Cysteines with Gromacs.
I've had tried different ways to combine the topology of both state A and
state B, and finally settled with the most direct way -- to mutate the
atoms that have different partial charges in the two states, and transform
the two hydrogen atoms into dummy atoms. As suggested by Gromacs manual
and some messages from the internet, I put explicitly the OPLS parameters
for the bonds, pairs, angles and dihedrals changed from state A to state B,
and the grompp didn't give a warning. But when I was testing the production
simulation on two processors, there was a warning of fatal error in the log
file:
=
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 3.774 nm, LJC Pairs NB, atoms 12 205
multi-body bonded interactions: 0.640 nm, Ryckaert-Bell., atoms 1013 417
Minimum cell size due to bonded interactions: 4.151 nm
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 2 cells with a minimum initial size of 5.189 nm
The maximum allowed number of cells is: X 0 Y 0 Z 0
---
Program mdrun, VERSION 4.5.4
Source code file: domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 5.18876 nm
Change the number of nodes or mdrun option -rdd or -dds
as suggested by the log:
1] Change the number of nodes
or
2] mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
=
The atoms indexed 12 and 205 are a CD1 in Leu1 and another CB in Ala12
respectively. I checked the topology and found no entries containing both
these atoms. What's weird is that there's no way for these two atoms to have
bonded interactions, but it says in the log that they have a two-body bonded
interaction with a distance of 3.774 nm, which I cannot understand.
Does anyone have an explanation what this could mean? Any suggestion is
appreciated!
Thanks in advance!
Xiaoxiao He
Oct. 15, 2011
Attached are the input parameters for the production md:
=
-Input Parameters:
integrator = sd
nsteps = 200
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 10
comm_mode = Linear
nstlog = 100
nstxout = 10
nstvout = 10
nstfout = 10
nstcalcenergy = 10
nstenergy = 100
nstxtcout = 1000
init_t = 0
delta_t = 0.0005
xtcprec = 1000
nkx = 36
nky = 36
nkz = 36
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
nsttcouple = -1
epc = Berendsen
epctype = Isotropic
nstpcouple = 10
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[ 1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[ 2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[ 0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[ 1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[ 2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed = 815131
rlist = 1.3
rlistlong = 1.3
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.3
vdwtype = Switch
Re: [gmx-users] Normal Mode Analysis
On Sat, Oct 15, 2011 at 2:58 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I have couple of questions about some Gromacs features. 1- I'm looking for tutorial where I could find clear example of force fied based Normal Mode Analysis via Gromacs E.g on first step I would like to prepare structure of my protein in pereodic boundary conditions and conduct energy minimization ( I've already can do it). Next I'd like to conduct full-atomic Normal Mode analysis and obtain motion trajectories along some lowest frequency modes for futher visualization in VMD. Finally I'd like to obtain information about frequencies ( eigenvalues) of each mode as well as frequencies of each residue fluctuations along different modes. 2- Also I'm looking for possible ways to enhanse Gromacs efficiency eg via ussage of multi cores of my CPU. I've found possible sillution via MPI function but this way dowsnt work in my case. How I can activate hyperthreading function as well as other possible ways ? If you installed from src, during configure --enable-threads if you installed via some package management tools, I guess they would install this way by default. try: mdrun -t Thank you for your help James -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)
On Thu, Oct 13, 2011 at 5:16 PM, Ahmad Randy run_...@yahoo.com wrote: Hi All, I understand that there were already some discussions about new DSSP exec with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that this two DSSP and do_dssp do not compatible each other? I was running in Ubuntu 10.04, and this is what I got: do_dssp -f 300K.trr -s 300K.tpr -o dssp I choose 5 'Mainchain' Fatal error: Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ ddvDjL4J /dev/null 2 /dev/null I already set the export DSSP=/home/madndy/dssp/dssp, and also try the latest do_dssp.c (from gromacs-4.6) file for instalation. Still didn't work. Are there are any suggestion or correction in my step? Or what version of gromacs that work well with DSSP? Or should I get the older version of DSSP that work with do_dssp? And where can I find the older version of DSSP because I can't find the older version in: http://swift.cmbi.ru.nl/gv/dssp/ . http://biskit.pasteur.fr/install/applications/dssp You may click above link (untested, be careful). Thanx, Randy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] lipid membrane slicing
On Wed, Oct 12, 2011 at 1:20 AM, Poojari, Chetan c.pooj...@fz-juelich.dewrote: Hi, I have protein completely inserted into lipid membrane and would like to study order parameter around the protein as well as away from the protein. For this I would like to slice my membrane into parts. I tried the following command: g_order -s *.tpr -f *.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -sl 2 The output i get from this is as same as the one where i dont use -sl 2 flag and it also doesnt show the different parts it has used for order parameter calculation. Please can I know how to slice my lipid membrane so that i can study order parameter for each part separately. It seems that the lipid around the protein is not fixed, it's slowly flow (fluid). during some time interval, not exactly the same lipids around the protein. maybe another different group. so here -sl 2 won't serve well for what you wanna test. Kind Regards, chetan Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] snap shot
On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I run the simulation for 20 ns. I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. trjconv use -dt 5000 I don't want to save snap shot for 128 ion-pairs. How can I take average over 128 ion pairs and save snap shot for a single ion pair. I don't understand the average mean here? if you wanna get the average.pdb in some time interval try g_rmsf -ox -b -e you may wait for some other better answers. Basically I want to use classical md geometry for quatum chemical calculation. I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] A quick Q: How to get the history in make_ndx
Hi, How do I use the history input in the make_ndx prompt, such as before I input name 32 A2 name 33 A3 up arrow showed me: ^[[A Alt+up arrow showed me: ^[[1;3A Just curious, Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: topology error
On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA ithayar...@gmail.com wrote: only 59 particle variation found out of 230 ligand coordinates. On 8 October 2011 12:22, ITHAYARAJA ithayar...@gmail.com wrote: Dear Sir, I am actually simulating my protein with its ligand so I incorporated all ligand (3) coordinates to my protein .gro file and placed its .itp file also. I used gromas96 43a1 force field. I found following error when i was doing grompp for energy minimization. I went through FAQ and checked all but i couldn't find what exactly it was. So, I attached that files to you. I need your help to solve this Program grompp, VERSION 4.5.1 Source code file: grompp.c, line: 377 Fatal error: number of coordinates in coordinate file (GR_b4ion.gro, 66074) does not match topology (GR.top, 66015) I used to count the atom numbers in .gro file and manually modify the topology to make them match. -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] concentration distribution
On Sep 25, 2011, at 0:33, raj vvindv.vvi...@gmail.com wrote: Hello, I would like to calculate the concentration distribution of atoms along the x and y axis from the trajectory. Can anybody suggest me a tool to calculate this? g_rdf ?! regards, Raj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] error while install GMX4.5.5
On Thu, Sep 22, 2011 at 8:11 PM, zhongjin zhongjin1...@yahoo.com.cn wrote: The system is Rocks 4.3 (Mars Hill), and [hzj1000@ZhouGroup ~]$ rpm -aq |grep glibc glibc-kernheaders-2.4-9.1.100.EL glibc-2.3.4-2.36 glibc-headers-2.3.4-2.36 glibc-common-2.3.4-2.36 glibc-devel-2.3.4-2.36 [hzj1000@ZhouGroup ~]$ gcc -v Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/specs Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=i386-redhat-linux Thread model: posix gcc version 3.4.6 20060404 (Red Hat 3.4.6-8) My gcc version is 4.6.1 probably it's nothing to do with your problem. just probably you may wanna to undate your gcc. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] diferent version of gcc
2011/9/23 Víctor Bahamonde nicegrom...@live.cl Hello gmx users I have a question related to gromacs compilation in the same machine, are there any difference in the result of MD when I compile the same version of gromacs but with diferent version of gcc? also, gcc 4.1.x still broken? I use Debian 5 and Debian 6 on amd phenom II quad core. http://packages.debian.org/sid/gromacs http://packages.debian.org/wheezy/gromacs They have had already well built .deb ball there. Install from your favoriate package management. Thanks in advance. *Víctor E. Bahamonde Padilla Laboratorio de Fisicoquímica Molecular Departamento de Química Facultad de Ciencias Universidad de Chile Phone: 562-978-7443 vedua...@ug.uchile.cl* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] MD with membrane protein
On Thu, Sep 22, 2011 at 11:34 AM, elisa carli elisacarl...@gmail.comwrote: Dear All I'd like to perfom a MD simulation on a membrane protein using DLPC or DPPC system I've downloaded the API package from this link http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies DPPC.zip and DLPC.zip by schiu How can I use them? Where can I get a tutorial or commands illustrating the use of these packages? Thanks in advance Here is a rough procedure: http://www.nanoconductor.org/43A1-S3/ Took Chiu's DPPC.zip as an example. We use the speptide.pdb peptide from the gromacs tutorial (it's a bad choice to put it in the dppc, but we just try it). pdb2gmx_g -f speptide.pdb -o speptide.gro choose 9: GROMOS96 43a1 force field 1: SPCsimple point charge, recommended $ tail -1 dppc.gro 5.68585 5.60685 6.85739 To be as simple as possible here, we use the dimension of the dppc.gro editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2 -box 5.68585 5.60685 6.85739 now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide, the purpose of doing a simple energy minimization here just want to test the topol.top. it used 43A1-S3 force field (You can download from http://www.nanoconductor.org/43A1-S3/). The head of topol.top: ; Include forcefield parameters #include ffG43A1-S3.itp #include lipids_43A1-S3.itp The tail of topol.top: [ molecules ] ; Compound#mols Protein 1 DPPC 71 SOL 3205 I manually added DPPC 71. please copy the lipids_43A1-S3.itpffG43A1-S3.itp ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current directory, extra copy ff_dum.itp from some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working directory. I attached all those files in try.tar.gz https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Njhl=en_GB mdrun_g -v -deffnm em works well. -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] about non-writing issue
Hi, Very sporadically and also with high frequent, The job I submitted only running without writing (this job is not un-started one, mainly one I stopped and rerun). Before I thought I did not wait long enough, such as hours, but seriously after 3 or 8 hours, still running not writing. I ssh to each nodes, all is fully running. The storage is NFS, I/O flow can't be choked for hours. Really headache, sometimes it works. I have had no clue about it. Thanks for any suggestions, -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: about non-writing issue
Hi, It works now. Not write (just based on guess) might the md.log step such as is 1114 while use thread I noticed the actually run step started from 11135000 so I run until it can write to the md.log then switch to 1 node to run for a while, then switch to more nodes. But there might be some reason there which I don't know. Thanks, On Sun, Sep 18, 2011 at 4:35 PM, lina lina.lastn...@gmail.com wrote: Hi, Very sporadically and also with high frequent, The job I submitted only running without writing (this job is not un-started one, mainly one I stopped and rerun). Before I thought I did not wait long enough, such as hours, but seriously after 3 or 8 hours, still running not writing. I ssh to each nodes, all is fully running. The storage is NFS, I/O flow can't be choked for hours. Really headache, sometimes it works. I have had no clue about it. Thanks for any suggestions, -- Best Regards, lina -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: about non-writing issue
On Mon, Sep 19, 2011 at 11:31 AM, Jianguo Li ljg...@yahoo.com.sg wrote: I met the similar problem before, sometimes my job writes output, sometimes not. My cluster administrator fixed the problem and they told me that there were some problem at some compute nodes which my job unfortunately was dispatched to. Last time I contacted the administrator, he told me it's due to the restriction he set, I mean, I could only use limited nodes. He loosed the configuration a bit and it worked at that time. But later it has happened, I don't have convincing confidence to email root again. So just try to figure out slowly. Thanks for your answering, Jianguo -- *From:* lina lina.lastn...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Sunday, 18 September 2011 5:13 PM *Subject:* [gmx-users] Re: about non-writing issue Hi, It works now. Not write (just based on guess) might the md.log step such as is 1114 while use thread I noticed the actually run step started from 11135000 so I run until it can write to the md.log then switch to 1 node to run for a while, then switch to more nodes. But there might be some reason there which I don't know. Thanks, On Sun, Sep 18, 2011 at 4:35 PM, lina lina.lastn...@gmail.com wrote: Hi, Very sporadically and also with high frequent, The job I submitted only running without writing (this job is not un-started one, mainly one I stopped and rerun). Before I thought I did not wait long enough, such as hours, but seriously after 3 or 8 hours, still running not writing. I ssh to each nodes, all is fully running. The storage is NFS, I/O flow can't be choked for hours. Really headache, sometimes it works. I have had no clue about it. Thanks for any suggestions, -- Best Regards, lina -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] How do I examine the results didn't write issue
Hi, I am confused, why the job is running, but they did not write the .edr, .log .xtc ... files. Everything showed so normal, just not writing, when I used thread, all is fine, the writing is normal. just use mpi, I tried different nodes, still not work, now two hours later, still no writing, just running. Thanks for providing any clue for me to examine. -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] How do I examine the results didn't write issue
On Mon, Sep 12, 2011 at 8:33 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: Hi, I am confused, why the job is running, but they did not write the .edr, .log .xtc ... files. Everything showed so normal, just not writing, when I used thread, all is fine, the writing is normal. just use mpi, I tried different nodes, still not work, now two hours later, still no writing, just running. Thanks for providing any clue for me to examine. Sounds like your MPI implementation is broken or you haven't issued the command right. If you have a test command that you know should work, run that. Otherwise, it's impossible to know if the problem is with Gromacs or something external. If you compiled with threading support, but not MPI (in a separate binary) then MPI will not work on the thread-enabled executable. I suspected it's MPI issue, but couple of days ago it's fine, and the results was able to write. I installed both MPI and thread but with different prefix to distinguish. Thanks, -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] How do I examine the results didn't write issue
On Mon, Sep 12, 2011 at 8:35 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 12/09/2011 10:23 PM, lina wrote: Hi, I am confused, why the job is running, but they did not write the .edr, .log .xtc ... files. Everything showed so normal, just not writing, when I used thread, all is fine, the writing is normal. just use mpi, I tried different nodes, still not work, now two hours later, still no writing, just running. If you can run mdrun_threads -np 4 and get output and your mpirun -np 4 mdrun_mpi does not write output, then there must be something wrong with your MPI environment. Try another MPI program and see what it does. I guess I will drop an email to the administrator. might be an MPI issue. Thanks for your time, Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to modify the md. log
Hi, My job terminated due to the storage out of the quote given by administrator, here the md.log is unusual, so when I resume the job, the results won't append on it. but still running... Here is the tail of md.log, DD step 31424999 load imb.: force 20.8% pme mesh/force 1.936 Step Time Lambda 3142500062850.00.0 ...snip... DD step 31425999 load imb.: force 23.7% pme mesh/force 1.923 Step Time Lambda 3142600062852.00.0 ...snip... Kinetic En. Total EnergyTemperature [lina@hostname You may notice that the [lina@hostname] did not start in a new line. there is md_step31441735.cpt and md_prev.cpt what is the final step stored in the md_prev.cpt? How do I check ? are there some chance to resume? Thanks ahead, Best regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: how to modify the md. log
On Sat, Sep 10, 2011 at 5:05 PM, lina lina.lastn...@gmail.com wrote: Hi, My job terminated due to the storage out of the quote given by administrator, here the md.log is unusual, so when I resume the job, the results won't append on it. but still running... Here is the tail of md.log, DD step 31424999 load imb.: force 20.8% pme mesh/force 1.936 Step Time Lambda 3142500062850.00.0 ...snip... DD step 31425999 load imb.: force 23.7% pme mesh/force 1.923 Step Time Lambda 3142600062852.00.0 ...snip... Kinetic En. Total EnergyTemperature [lina@hostname You may notice that the [lina@hostname] did not start in a new line. there is md_step31441735.cpt and md_prev.cpt what is the final step stored in the md_prev.cpt? How do I check ? gmxcheck shows: Last frame -1 time 62400.328 End of file on md.xtc but not on md_prev.cpt Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] radial distribution function
On Sat, Sep 10, 2011 at 10:00 PM, Moeed lecie...@googlemail.com wrote: Thank you for your input. I am going to run for another 15 ns to see if the little jumps vanish. Best, g_rdf -bin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to modify the md. log
On Sat, Sep 10, 2011 at 8:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: Hi, My job terminated due to the storage out of the quote given by administrator, here the md.log is unusual, so when I resume the job, the results won't append on it. but still running... Here is the tail of md.log, DD step 31424999 tel:31424999 load imb.: force 20.8% pme mesh/force 1.936 Step Time Lambda 31425000 tel:3142500062850.00.0 ...snip... DD step 31425999 tel:31425999 load imb.: force 23.7% pme mesh/force 1.923 Step Time Lambda 31426000 tel:3142600062852.00.0 ...snip... Kinetic En. Total EnergyTemperature [lina@hostname You may notice that the [lina@hostname] did not start in a new line. there is md_step31441735.cpt and md_prev.cpt what is the final step stored in the md_prev.cpt? How do I check ? It should be the step -cpt minutes before the later checkpoint was written. Use gmxcheck to verify its contents. are there some chance to resume? Make sure the existing job has been killed (which sounds like it may or may not be the case) and simply restart from the appropriate checkpoint. http://www.gromacs.org/**Documentation/How-tos/Doing_**Restartshttp://www.gromacs.org/Documentation/How-tos/Doing_Restarts -Justin Thanks. -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] md.mdp file GPU one
Hi, are there someone love to share one md.mdp file for GPU version? Thanks ahead, -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] md.mdp file GPU one
On Fri, Sep 9, 2011 at 8:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: Hi, are there someone love to share one md.mdp file for GPU version? All the details are here: http://www.gromacs.org/**Downloads/Installation_** Instructions/GPUs?highlight=**gpuhttp://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu The benchmark archive has example .mdp files that you can tweak. Thanks. ( From those warnings, started to realize its limitations, no plan to try further recently. ^_^ ) -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] radial distribution function
On Sat, Sep 10, 2011 at 3:35 AM, Moeed lecie...@googlemail.com wrote: Dear users, I have created radial distribution function plot for Carbon atoms in a system containing polymer chains. I see some little jumps between first and second peak. I need your help to comment on how this behavior can be justified (or if the plot is wrong). g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx Thank you in advance. I think your figure is fine. You just need how to proper interpret your figures, truly understand what the radial distribution means. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] no output in g_dist
On Thu, Sep 8, 2011 at 8:25 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, To get the distance between water and protein i did - g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11 from this i should obtain an output file as distance.xvg which i dont get. The -dist option: Print all atoms in group 2 (water) closer than dist to the center of mass of group 1 (protein in your case). As you have seen, it *print* the result on the screen. To obtain the distance.xvg file, please don't use the -dist option here. and my output is printed on the terminal as- t: 1 136 SOL 2336 OW 0.772373 (nm) t: 1 136 SOL 2337 HW1 0.706358 (nm) t: 1 136 SOL 2338 HW2 0.807787 (nm) t: 1 139 SOL 2345 OW 0.821094 (nm) t: 1 139 SOL 2346 HW1 0.810919 (nm) t: 1 139 SOL 2347 HW2 0.771526 (nm) t: 1 7237 SOL 23640 HW1 0.997056 (nm) t: 1 11793 SOL 37307 OW 0.868929 (nm) t: 1 11793 SOL 37308 HW1 0.927205 (nm) t: 1 11793 SOL 37309 HW2 0.776699 (nm) t: 2 125 SOL 2303 OW 0.940527 (nm) In this t: 1 136 SOL 2336 OW 0.772373 (nm) does the 't' states the time frame, 136 SOL states the SOL molecule number and 2336 OW the residue contact from protein and the 0.772373 nm the distance between them. Thanks -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] termini modification
pdb2gmx -ter On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj vijayara...@gmail.com wrote: Hello, I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the terminal residues from NALA and CALA to normal ALA (just as middle residues). As the terminal selection option is not enabled with the amber ff, I am using the termini modification parameters with aminoacids.c.tdb. here is my code for the aminoacids.c.tdb [ COO- ] [ replace ] H H 1.00800 0.27190 N N 14.01000 -0.41570 CA CT 12.01000 0.03370 HA H1 1.00800 0.08230 C C 12.01000 0.59730 CB CT 12.01 -0.1825 HB1 HC 1.008 0.0603 HB2 HC 1.008 0.0603 HB3 HC 1.008 0.0603 [ add ] 1 1 O C CA N O 16.0 -0.56790 [ bonds ] C O 1 0.12290 476976.0 [ delete ] OC1 OC2 when I run pdb2gmx using this termini modification, everything works fine except the deletion of OC1 and OC2 atoms, the error which I get for this run as follows, Fatal error: Atom OC2 not found in residue seq.nr. 8 while adding atom any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [ delete ] option with the aminoacids.c.tdb file, it works fine by adding the O atom to the terminal residue including the presence of OC1 and OC2 atoms. first I am trying to modify the c terminal residue. Regards, vijay. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding g_sham
On Sat, Aug 13, 2011 at 3:36 PM, bipin singh bipinel...@gmail.com wrote: Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata Sorry, I am not sure what's kind of full description you expect, Try: g_sham -h or man g_sham -- --- Regards, Bipin Singh -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'
On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers breue...@uni-koeln.de wrote: Dear all, searching for the mentioned error message I found a bug report for mdrun. It seemed to be fixed, but in my setup it appears again and I am not sure if I could do something about it. I did not attach the tpr file since it is bounced by the mailing list and I'd like to get at least a hint without waitng for approval of the rejected mail. :) The simulation crashes with 64 CPUs after step 11237000 with the following entry in the log file: --- Program mdrun, VERSION 4.5.4 Source code file: /home/breuerss/local/src/gromacs-4.5.4/src/mdlib/domdec_top.c, line: 352 Software inconsistency error: One or more interactions were multiple assigned in the domain decompostion For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That means that the simulation already ran for some time. I could also finish some runs successfully with the very same topology but different simulation parameters. For any help or hints how I could fix it I would be grateful. Have you tried to re-submit it, use the -cpi state.cpt -append and see whether it can continue or not? Best regards Sebastian -- _ Sebastian Breuers Tel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für Chemie Department of Chemistry Organische Chemie Organic Chemistry Greinstraße 4 Greinstraße 4 Raum 325 Room 325 D-50939 Köln D-50939 Cologne, Federal Rep. of Germany _ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to calculate the conc in the genion
Hi, after using genion -conc 0.1 certain number of Na and Cl were added in solvent. but when I tried to calculate back, namely, based on the number of Na and Cl, the number of water molecular and the box volumn, but seems can't come back, I mean, can't obtain the result of 0.1mol/L. I read the manual, ...the specified concentration as computed from the volume of the cell... the cell? Has anyone tried to calculate the concentration back? ( I guess might the way I calculate was wrong? the Avogadro's Constant = 6.0221415 × 10^23 mol-1) Thanks with best regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
