[gmx-users] what is the eigenvalue unit in Gromacs?
Dear all, I used g_nmeig to diagonalize the Hessian matrix, that I got the eigenvalues. However, I found that in the file 'eigenval.xvg' the unit of the eigenvalues are Eigenvalue [Gromacs units]. What is the '[Gromacs units]'? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about how to install g_tune_pme
Hi Yi,
the most convenient way in my opinion is to copy the
Makefile.arch from the already installed gromacs-4.0.7
version and copy it into the directory where g_tune_pme.c
is. Rename Makefile.arch to Makefile and inside it
exchange the three occurences of template by g_tune_pme.
Type make and you are going to get a g_tune_pme
executable which you can copy to the installed gromacs-4.0.7
bin directory. If you also copy the provided completion.*
files to the gromacs bin directory, tab completion will also
work for g_tune_pme.
Example:
Let's assume gromacs is installed in /usr/local/gromacs/407/
tar -xvf g_tune_pme.tgz
cd tune
cp
/usr/local/gromacs/407/share/gromacs/template/Makefile.x86_64-unknown-linux-gnu
.
cat Makefile.x86_64-unknown-linux-gnu | sed {s/template/g_tune_pme/g} Makefile
make
cp g_tune_pme /usr/local/gromacs/407/bin
cp completion.* /usr/local/gromacs/407/bin
That should do the trick.
Best,
Carsten
On Jun 10, 2010, at 11:02 PM, Yi Peng wrote:
Hi, Everyone,
We want to install g_tune_pme tool to our Gromacs-4.0.7 on our cluster. We
don't know which Makefile in the template directory we should use, should we
run make in the tune directory, or even configure, or should we compile this
together with gromacs? Should we use mpi library? which one?Thanks a lot.
Yi
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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[gmx-users] pressure scaling more than 1%
Hi all, my simulation runs well for the first 70 steps with a step size of 0.001ps and when I get the warning that the pressure scaling is more than 1% every 1 step or so. So, is my tau_p of 0.2 to small or is the equillibration not done well enough. I am simulating a small peptide in CHCl3 with an handmade CHCl3 model. title= ttt cpp = /lib/cpp include = -I../top constraints = none ;define = -DFLEX_SPC ;define = -DPOSRES; for possition restraints integrator = md emtol = 100.0 emstep = 0.005 dt = 0.001; ps ! nsteps = 200 ; total 2 ns nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 10 nstlog = 0 nstenergy = 10 nstxtcout = 10 xtc_grps= Protein+PTS+AIC nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb= 1.2 rvdw= 1.2 fourierspacing = 0.12 pme_order = 4 optimize_fft= yes Tcoupl = berendsen tc-grps = Protein+PTS+AIC CHCl3 tau_t = 0.1 0.1 ref_t = 300 300 energygrps = Protein+PTS+AIC CHCl3 Pcoupl = berendsen tau_p = 0.2 compressibility = 5.4e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 913529 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf -res
Hi Tsjerk, thank you for your answer. Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation. But I have another question: I need to take 3 structures and make an average structure of these 3. Is there a way to do it with gromacs? Cheers, Carla On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous carlajam...@gmail.com wrote: Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. Single structures (initial c.q. average) do not have an RMSF. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf This is not what you did. Please copy/paste command lines. I got the same result, when choosing C-alpha for root mean square calculation. Sure, when selecting C-alphas, averaging the RMSF per residue (sum_over_calphas_in_residue/number_of_calphas_in_residue) will evidently be identical to calculating the RMSF on an atom basis for each Calpha. So please can anyone explain how can I get the average per residue over a period of time? Select 'protein' (and use the -res flag). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf -res
Hi, yes it can be done with g_covar, but such an average structure is often of little physical significace. Imagine for instance the acerage structure of a rotating methyle group (it's a bunch of atoms on a line). Erik Carla Jamous skrev: Hi Tsjerk, thank you for your answer. Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation. But I have another question: I need to take 3 structures and make an average structure of these 3. Is there a way to do it with gromacs? Cheers, Carla On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous carlajam...@gmail.com mailto:carlajam...@gmail.com wrote: Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. Single structures (initial c.q. average) do not have an RMSF. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf This is not what you did. Please copy/paste command lines. I got the same result, when choosing C-alpha for root mean square calculation. Sure, when selecting C-alphas, averaging the RMSF per residue (sum_over_calphas_in_residue/number_of_calphas_in_residue) will evidently be identical to calculating the RMSF on an atom basis for each Calpha. So please can anyone explain how can I get the average per residue over a period of time? Select 'protein' (and use the -res flag). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf -res
Please does anyone know how is calculated the B factor in gromacs? What is the formula that gives the B factor with the average coordinates with g_rmsf? Carla On Fri, Jun 11, 2010 at 10:53 AM, Erik Marklund er...@xray.bmc.uu.sewrote: Hi, yes it can be done with g_covar, but such an average structure is often of little physical significace. Imagine for instance the acerage structure of a rotating methyle group (it's a bunch of atoms on a line). Erik Carla Jamous skrev: Hi Tsjerk, thank you for your answer. Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation. But I have another question: I need to take 3 structures and make an average structure of these 3. Is there a way to do it with gromacs? Cheers, Carla On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar tsje...@gmail.commailto: tsje...@gmail.com wrote: Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous carlajam...@gmail.com mailto:carlajam...@gmail.com wrote: Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. Single structures (initial c.q. average) do not have an RMSF. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf This is not what you did. Please copy/paste command lines. I got the same result, when choosing C-alpha for root mean square calculation. Sure, when selecting C-alphas, averaging the RMSF per residue (sum_over_calphas_in_residue/number_of_calphas_in_residue) will evidently be identical to calculating the RMSF on an atom basis for each Calpha. So please can anyone explain how can I get the average per residue over a period of time? Select 'protein' (and use the -res flag). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Coulomb (SR) problem
hello again I had a problem with a sim of some molecules in vacuum and a gmx-user told me to do a simulation only in one molecule just to see what gromacs calculates and what does not. My problem concerned the sum of all energies in the system. After i did the sim with one molecule i found out that either gromacs either me calculate the Coulomb SR(short range) energy wrong. so for step 0 of this simulation I had this result: Started mdrun on node 0 Fri Jun 11 12:52:33 2010 Step Time Lambda 0 0.0 0.0 Grid: 3 x 3 x 3 cells Long Range LJ corr.: C6 3.8522e-03 Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol) Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR) 5.70627e+00 8.37083e+00 6.80805e-03 1.72679e+02 -3.25801e+00 Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En. -7.32091e-03 -2.93587e+01 -1.21273e+02 3.28661e+01 3.94838e+01 Total Energy Temperature Pressure (bar) Cons. rmsd () 7.23499e+01 3.65291e+02 4.25496e+01 3.53180e-07 so as you can see the value of Coulomb (SR) is -2.93587e+01 and my calculation is -1302.68 I believe that even i have done wrong calculations the value that gromacs finds is not correct. I found this value from the formula sum(f*qi*qj/rij) for every atom pair like 1-2,1-3,(not the 1-4),1-5etc 2-3,2-4(not 1-2 because it is already calculated) etc ...3-.etc. inside the rcoulomb (the whole molecule) where f is the electric conversion factor f=138,935kJmol-1*nm*e-2 IS COULOMB (SR) calculated that way by hand??? i an using PME btw i have not done arithmetic mistake i am sure for that (at least :) ) Please consider that: 1) I dont use ffXXX.itp libraries from gromacs i have my own 2) I have tried every possible way to do this simulation for the past 3 months (its my problem i know that !!! :) ) 3) I have calculated the coulomb 1-4 with success and great accuracy 4) I have also caclulated the LJ (SR) with success (irrelevant!!!) :) 5) i am using gromacs 4.05 Please if you have smth to advise me about this simulation except committing suicide of course :) please feel free to do it Thanks in advance especially Mark Abraham who helped my at first place -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Coulomb (SR) problem
On 2010-06-11 12.13, Thanasis Koukoulas wrote: hello again I had a problem with a sim of some molecules in vacuum and a gmx-user told me to do a simulation only in one molecule just to see what gromacs calculates and what does not. My problem concerned the sum of all energies in the system. After i did the sim with one molecule i found out that either gromacs either me calculate the Coulomb SR(short range) energy wrong. so for step 0 of this simulation I had this result: Started mdrun on node 0 Fri Jun 11 12:52:33 2010 Step Time Lambda 0 0.0 0.0 Grid: 3 x 3 x 3 cells Long Range LJ corr.: C6 3.8522e-03 Long Range LJ corr.: Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol) Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR) 5.70627e+00 8.37083e+00 6.80805e-03 1.72679e+02 -3.25801e+00 Disper. corr. Coulomb (SR) Coul. recip. Potential Kinetic En. -7.32091e-03 -2.93587e+01 -1.21273e+02 3.28661e+01 3.94838e+01 Total Energy Temperature Pressure (bar) Cons. rmsd () 7.23499e+01 3.65291e+02 4.25496e+01 3.53180e-07 so as you can see the value of Coulomb (SR) is -2.93587e+01 and my calculation is -1302.68 You should turn off PME and set the cutoffs to zero in this case. I believe that even i have done wrong calculations the value that gromacs finds is not correct. I found this value from the formula sum(f*qi*qj/rij) for every atom pair like 1-2,1-3,(not the 1-4),1-5etc 2-3,2-4(not 1-2 because it is already calculated) etc ...3-.etc. inside the rcoulomb (the whole molecule) where f is the electric conversion factor f=138,935kJmol-1*nm*e-2 IS COULOMB (SR) calculated that way by hand??? i an using PME btw i have not done arithmetic mistake i am sure for that (at least :) ) Please consider that: 1) I dont use ffXXX.itp libraries from gromacs i have my own 2) I have tried every possible way to do this simulation for the past 3 months (its my problem i know that !!! :) ) 3) I have calculated the coulomb 1-4 with success and great accuracy 4) I have also caclulated the LJ (SR) with success (irrelevant!!!) :) 5) i am using gromacs 4.05 Please if you have smth to advise me about this simulation except committing suicide of course :) please feel free to do it Thanks in advance especially Mark Abraham who helped my at first place -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] restarting simulation
Hi all For restarting a crashed simulation, do you have to use the -s topol.tpr in the command below. I have left it out and everything seems to be O.K. I'm just double checking though. mdrun -s topol.tpr -cpi state.cpt -append -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restarting simulation
Gavin Melaugh wrote: Hi all For restarting a crashed simulation, do you have to use the -s topol.tpr in the command below. I have left it out and everything seems to be O.K. I'm just double checking though. mdrun -s topol.tpr -cpi state.cpt -append If you're using default filenames, if you omit the -s flag, mdrun will look for topol.tpr anyway. -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/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restarting simulation
Thanks guys XAvier Periole wrote: On Jun 11, 2010, at 3:30 PM, Gavin Melaugh wrote: Hi all For restarting a crashed simulation, do you have to use the -s topol.tpr in the command below. I have left it out and everything seems to be O.K. I'm just double checking though. mdrun -s topol.tpr -cpi state.cpt -append -s topol.tpr is the default option so it never has to be specified unless you use a different name than topol.tpr. so the answer is no :)) but it does not matter -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] top2psf.pl
Hi Trying to use top2psf.pl, as suggested Usage: top2psf.pl -i (topology filename) -o (output filename) but I get an error message saying invalid command name top2psf.pl Suggestions? Thanks Rabab -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pressure scaling more than 1%
Sebastian Waltz wrote: Hi all, my simulation runs well for the first 70 steps with a step size of 0.001ps and when I get the warning that the pressure scaling is more than 1% every 1 step or so. So, is my tau_p of 0.2 to small or is the equillibration not done well enough. Possibly, have you tried larger values? Usually something on the order of 1.0-5.0 ps is more typical. I am simulating a small peptide in CHCl3 with an handmade CHCl3 model. If you're seeing instabilities, it could also be related to the topology. Have you thoroughly validated the parameters you're using for CHCl3? -Justin title= ttt cpp = /lib/cpp include = -I../top constraints = none ;define = -DFLEX_SPC ;define = -DPOSRES; for possition restraints integrator = md emtol = 100.0 emstep = 0.005 dt = 0.001; ps ! nsteps = 200 ; total 2 ns nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 10 nstlog = 0 nstenergy = 10 nstxtcout = 10 xtc_grps= Protein+PTS+AIC nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb= 1.2 rvdw= 1.2 fourierspacing = 0.12 pme_order = 4 optimize_fft= yes Tcoupl = berendsen tc-grps = Protein+PTS+AIC CHCl3 tau_t = 0.1 0.1 ref_t = 300 300 energygrps = Protein+PTS+AIC CHCl3 Pcoupl = berendsen tau_p = 0.2 compressibility = 5.4e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 913529 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/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] combine position restraints and NPT equlibration in membrane
In God We Trust Hello Dear GMX users We would like to perform MD simulation of a protein in attendance of biomembrane (POPE). On the basis of Kalp tutorial, can we combine position restraints and NPT equlibration in one phase?. We attached NPT.mdp in this mail. Please guide us. Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ npt.mdp Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Help! --- Permission denied (publickey, gssapi-with-mic, password).
Hi There, Please help me with this permission issue! Thanks. (Below are the input and output, followed by the information of my compiling procedure) #!/bin/csh -f #$ -cwd #$ -N gro.t.4 #$ -S /bin/tcsh #$ -l h_rt=120:00:00 #$ -e SGE.err #$ -o SGE.out #$ -pe mpich 4 mpirun -np 4 mdrun_mpi -s topol.tpr -o output_test.trr -e topol.tpr -x output_test.trr -catch_rsh /opt/gridengine/default/spool/compute-2-9/active_jobs/424509.1/pe_hostfile compute-2-9 compute-2-9 compute-2-21 compute-2-21 Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. ## /home/y1gao/soft/openmpi-1.4.2/bin/mpirun libopen-rte.so.0 = /home/y1gao/soft/openmpi-1.4.2/lib/libopen-rte.so.0 (0x40001000) libopen-pal.so.0 = /home/y1gao/soft/openmpi-1.4.2/lib/libopen-pal.so.0 (0x40078000) libnuma.so.1 = /usr/lib/libnuma.so.1 (0x004cf000) libdl.so.2 = /lib/libdl.so.2 (0x400d7000) libnsl.so.1 = /lib/libnsl.so.1 (0x0054c000) libutil.so.1 = /lib/libutil.so.1 (0x00516000) libm.so.6 = /lib/tls/libm.so.6 (0x004d5000) libgcc_s.so.1 = /lib/libgcc_s.so.1 (0x0050c000) libpthread.so.0 = /lib/tls/libpthread.so.0 (0x005ed000) libc.so.6 = /lib/tls/libc.so.6 (0x003a2000) libimf.so = /nas/y1gao/soft/intel-11.1.072/lib/ia32/libimf.so (0x400dc000) libsvml.so = /nas/y1gao/soft/intel-11.1.072/lib/ia32/libsvml.so (0x40341000) libintlc.so.5 = /nas/y1gao/soft/intel-11.1.072/lib/ia32/libintlc.so.5 (0x4046c000) /lib/ld-linux.so.2 (0x00384000) /home/y1gao/soft/gromacs-4.0.5/bin/mdrun_mpi libnsl.so.1 = /lib/libnsl.so.1 (0x0054c000) libm.so.6 = /lib/tls/libm.so.6 (0x004d5000) libSM.so.6 = /usr/X11R6/lib/libSM.so.6 (0x004fa000) libICE.so.6 = /usr/X11R6/lib/libICE.so.6 (0x00611000) libX11.so.6 = /usr/X11R6/lib/libX11.so.6 (0x40008000) libmpi.so.0 = /home/y1gao/soft/openmpi-1.4.2/lib/libmpi.so.0 (0x400e7000) libopen-rte.so.0 = /home/y1gao/soft/openmpi-1.4.2/lib/libopen-rte.so.0 (0x40299000) libopen-pal.so.0 = /home/y1gao/soft/openmpi-1.4.2/lib/libopen-pal.so.0 (0x4031) libnuma.so.1 = /usr/lib/libnuma.so.1 (0x004cf000) libdl.so.2 = /lib/libdl.so.2 (0x40368000) libutil.so.1 = /lib/libutil.so.1 (0x00516000) libgcc_s.so.1 = /lib/libgcc_s.so.1 (0x0050c000) libpthread.so.0 = /lib/tls/libpthread.so.0 (0x005ed000) libc.so.6 = /lib/tls/libc.so.6 (0x003a2000) /lib/ld-linux.so.2 (0x00384000) libimf.so = /nas/y1gao/soft/intel-11.1.072/lib/ia32/libimf.so (0x4036d000) libsvml.so = /nas/y1gao/soft/intel-11.1.072/lib/ia32/libsvml.so (0x405d2000) libintlc.so.5 = /nas/y1gao/soft/intel-11.1.072/lib/ia32/libintlc.so.5 (0x406fc000) ## --- Warning: Permanently added 'compute-2-21.local' (RSA) to the list of known hosts. Permission denied, please try again. Permission denied, please try again. Permission denied (publickey,gssapi-with-mic,password). -- A daemon (pid 11510) died unexpectedly with status 129 while attempting to launch so we are aborting. There may be more information reported by the environment (see above). This may be because the daemon was unable to find all the needed shared libraries on the remote node. You may set your LD_LIBRARY_PATH to have the location of the shared libraries on the remote nodes and this will automatically be forwarded to the remote nodes. -- -- mpirun noticed that the job aborted, but has no info as to the process that caused that situation. -- mpirun: clean termination accomplished I got this error when I started the parallel runs of the gromacs on the cluster via MPI. My compiling procedure was: intel_fortran_11.1.072 -- intel_c++_11.1.072 -- openmpi 1.4.2-- fftw3.2.2 -- gromacs4.0.5 (LAM/MPI was already installed but does not work properly.) -- Yan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Disk Space
Dear Gromacs users, I am running an MD simulation but it looks to me that I am running out of disk space. This is my .mdp file ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 100 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file nstxtcout= 100 xtc-precision= 100 nstcheckpoint= 100 ; checkpointing helps you continue after crashe. This checkpint file is saved every 1ns Please tell me which files i need to set zero. I am planning to run my simulation for 20ns but I want it to run every five nanoseconds until i see an aggregations in my system. So how can I re-start my simulation every 5ns. Thank you for your help rob -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Selecting specific atoms to find average energy of
Hello, I ran an md simulation, and I have graphed the total average energy of the system by using g_energy to convert my binary .edr file into a text based file. What I want to do is to find the average energy between the solvent molecules, excluding the energy between the solute-solvent molecules and the solute-solute molecules. I was unable to find a way to have g_energy give me the energy between a specific group. Is it possible to do this? Or do I need to rerun the simulation, and include something like energy monitor groups? There is probably a simple command for this that I am missing (or at least I hope there is). I would prefer not to have to rerun all of my md simulations. Thanks in advance, Jennifer -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Disk Space
Dear Rob: To answer your question: just set up your run with nsteps for 5 ns, run mdrun, and then use tpbconv -until. A simpler option is to set it up to run 20 ns, but use -maxh to limit it to an amount of runtime that you pre-calculate to be similar to 5 ns of simulation. HOWEVER: You almost surely don't need to save this so often: nstxout = 100 (also nstvout, nstfout). And you may not even need to save this so often: nstxtcout = 100 (also nstenergy). I had no idea that there was an option nstcheckpoint = 100 as I use mdrun -cpt 6 to specify a .cpt file every 6 hours, but there is no need to write a .cpt every 100 steps. Dear Gromacs users, I am running an MD simulation but it looks to me that I am running out of disk space. This is my .mdp file ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 100 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file nstxtcout= 100 xtc-precision= 100 nstcheckpoint= 100 ; checkpointing helps you continue after crashe. This checkpint file is saved every 1ns Please tell me which files i need to set zero. I am planning to run my simulation for 20ns but I want it to run every five nanoseconds until i see an aggregations in my system. So how can I re-start my simulation every 5ns. Thank you for your help rob -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on CYGWIN
Also, use the 'nice' command to run gmx at high priority, and switch off CPU frequency scaling. For me, cygwin performance is pretty much the same as that on linux, which is to be expected since most of the code isn't dependent on system calls. Apparently, the only difference you should be able to see is in disk I/O, but you don't want to I/O too frequently anyway. On Fri, Jun 11, 2010 at 3:18 AM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Nasim Biglari nasim...@yahoo.co.uk Date: Friday, June 11, 2010 2:51 Subject: [gmx-users] GROMACS on CYGWIN To: gmx-users@gromacs.org Dear all, I was wondering whether GROMACS on CYGWIN is less capable than GROMACS run on LINUX? i.e. concerning its speed and its ability to simulate larger macromolecules. I assume that it is faster, but is it very much different? GROMACS will run fine, and do approximately the same under either OS on comparable hardware with the same version of gcc, however for production simulation to be maximally effective you need to arrange for the simulation process not to be interrupted much. This is easier to arrange on Linux than Windows. You certainly don't want to be concurrently using either kind of machine as a desktop, and also you'd prefer not to be logged on to either machine. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] combine position restraints and NPT equlibration in membrane
Quoting Mahnam mah...@ibb.ut.ac.ir: In God We Trust Hello Dear GMX users We would like to perform MD simulation of a protein in attendance of biomembrane (POPE). On the basis of Kalp tutorial, can we combine position restraints and NPT equlibration in one phase?. We attached NPT.mdp in this mail. Please guide us. In the tutorial, position restraints are applied during both NVT and NPT equilibration, with the purpose of separately equilibrating temperature and pressure. You could try to do both in one NPT run, but in my experience, POPE requires some finesse during equilibration, so two phases are probably best. -Justin Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Selecting specific atoms to find average energy of
Quoting Jennifer Casey jrcase...@gmail.com: Hello, I ran an md simulation, and I have graphed the total average energy of the system by using g_energy to convert my binary .edr file into a text based file. What I want to do is to find the average energy between the solvent molecules, excluding the energy between the solute-solvent molecules and the solute-solute molecules. I was unable to find a way to have g_energy give me the energy between a specific group. Is it possible to do this? Or do I need to rerun the simulation, and include something like energy monitor groups? There is probably a simple command for this that I am missing (or at least I hope there is). I would prefer not to have to rerun all of my md simulations. You will have to rerun your simulations using a new .tpr file with the desired energygrps defined. The good news is that you simply have to rerun the trajectory using mdrun -rerun, which is substantially faster than recalculating the whole thing from scratch. -Justin Thanks in advance, Jennifer Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
