Re: [gmx-users] entropy vs time plot
On 2014-05-21 06:54, tarak karmakar wrote:
Hi Tsjerk,
Thanks for the quick reply.
I did the following
g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v
eigenvec.trr -av average.pdb -b 0 -e 1
g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 1
What I want to plot is similar to this.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/
Is there any flag for this?
I've checked g_covar -h and g_anaeig -h but didn't get the proper way.
You need to run a
for($N=1000; ($N=1); $N+= 100) {
g_covar -e $N
g_anaeig
grep S from standard out and save it
}
Thanks,
Tarak
On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi Tarak,
You will have to use -b/-e to set the start and end times.
Cheers,
Tsjerk
On Tue, May 20, 2014 at 12:18 PM, tarak karmakar tarak20...@gmail.com
wrote:
Dear All,
Could anyone tell me how to plot configurational entropy as a function of
simulation time?
Do I need to manually specify the -dt(say after each 1 ns) during the
g_covar and then do g_anaeig in each of the step?
thanks,
Tarak
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Re: [gmx-users] topology in local?
Dear Nicola, Any number of users can use the top directory, with the choice of his/her force field. If anyone wants to edit the top files, then he can copy the top directory to somewhere and use the GMXLIB variable. You can use the GMXLIB environment variable, and point your top directory's path to it. For more details refer http://www.gromacs.org/Documentation/Terminology/Environment_Variables. Chandan On Wed, May 21, 2014 at 2:52 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear GROMACS user community, I have the following problem: I would like to let a simulation run on a computer where another simulation, prepared by another user, is already running; my simulation and the simulation of the other user need different topologies (I mean, for example, the files ffbonded.itp and ffnonbonded.itp files stored in /usr/share/gromacs/top/forcefield.ff are different; or, to make things more clear, let's suppose as a condition that user 1 needs to use charmm27.ff and user 2 gromos43a1.ff). Does anybody know of any solution where the number of computers is kept constant? What would happen, for example, if I would put my topology files inside my local working directory? Thank you very much in advance, Nicola -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Hey Vito, Can you paste your exact workflow? Cheers, Tsjerk On Wed, May 21, 2014 at 9:53 AM, Vito Genna vito.ge...@iit.it wrote: Hi Tsierk, Hi tried your protocol without success. I have also tried different centering combination (on protein/DNA/Ligand/Protein+DNA/DNA+Ligand/Protein+ligand) and different flags combo (-pbc mol -ur compact/rect). I have added also the pbc whole before -pbc nojump but the result at the end is always the same, as shown in fig http://wikisend.com/download/185858/fig5.png The bonds are disappeared it's a god start but it is not enough to make measurements inside the catalytic pocket. I hope to find a solution with you and to write down a protocol for people which work whit ternary complexes. Thank you for your time. Best Regards V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, May 20, 2014 9:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, If the .tpr file is good, i.e. has everything assembled the way you want, then the first step is trjconv -pbc nojump. That will make sure that nothing gets split over PBC. Then center the protein in the box (trjconv -center), and subsequently put all molecules in the box (-pbc mol -ur compact/rect). Cheers, Tsjerk On Tue, May 20, 2014 at 7:51 PM, Vito Genna vito.ge...@iit.it wrote: Hi Tsjerk, Thank you for your email. No it is not broken. The structure is intact till the 20 ns of production phase. I have already used the .tpr (both md_0_1.tpr before, and then npt.tpr) obtaining the same result. Basically you are suggesting to fix the first frame of the production phase and use it as a reference point for the subsequent manipulations (-pbs nojump) of all TRJs? I'm going to do this attempt and I will keep you posted. Thanks again. Cheers V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, May 20, 2014 7:30 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, Was the structure already broken up when you solvated it? If not, which seems likely to me, then you can use that structure, or the .tpr from the EM in solvent, to remove jumps from the first frame of your run. After you unbroke the first frame, you can use that as reference for processing your trajectory with -pbc nojump. Hope it helps, Tsjerk On Tue, May 20, 2014 at 7:14 PM, Vito Genna vito.ge...@iit.it wrote: Dear Justin, Thank you for your email. As in your case, my system is formed by a Protein + dsDNA + structural ions + counterions + ligand + water I guess that I have too much element to efficiently solve the problem but I want to try to fix it. The solution could help other people to avoid to became crazy with this kind of TRJs manipulations. Figs. link: http://wikisend.com/download/571570/pics.zip Well. today I tried a different combo as: A) trjconv -s -f -pbc mol(res) -center (-n index with DNAProtein/Ligand/Protein) to obtain trajectories as shown in pic1 B) Then i used -pbc whole/nojump to obtain a result as shown in fig 2 I guess that the problem still persists Any suggestion about your experience? Thanks in advance V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
Re: [gmx-users] topology in local?
On 5/21/14, 5:22 AM, Nicola Staffolani wrote: Dear GROMACS user community, I have the following problem: I would like to let a simulation run on a computer where another simulation, prepared by another user, is already running; my simulation and the simulation of the other user need different topologies (I mean, for example, the files ffbonded.itp and ffnonbonded.itp files stored in /usr/share/gromacs/top/forcefield.ff are different; or, to make things more clear, let's suppose as a condition that user 1 needs to use charmm27.ff and user 2 gromos43a1.ff). Does anybody know of any solution where the number of computers is kept constant? What would happen, for example, if I would put my topology files inside my local working directory? Once grompp is invoked, the force field files in $GMXLIB (or anywhere else, for that matter) are irrelevant; everything mdrun needs is in the .tpr file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] grompp
Dear Gromacs users, I am new to Gromacs. I am trying to add ions to my protein system. After typing command: grompp -f grompp.mdp -c EcoLon6mer-sol.gro -p EcoLon6mer.top -o genion_input.tpr where the grompp.mdp contains: ; ions.mdp - used as input into grompp to generate ions.tpr ; 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 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) I am getting an error message: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# checking input for internal consistency... processing topology... Opening library file /software/local/Gromacs/4.5.3/Intel-ompi-fftw/share/gromacs/top/amber99.ff/forcefield.itp --- Program grompp, VERSION 4.0.7 Source code file: futil.c, line: 526 Fatal error: Library file ffnonbonded.itp not found in current dir nor in your GMXLIB path. --- Disturb the Peace of a John Q Citizen (Urban Dance Squad) How can I solve this problem? How can I add the path? best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology in local?
Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? From what I have read about environment variableshttp://en.wikipedia.org/wiki/Environment_variable#Unix, if another simulation is already running on a computer and I want to launch my simulation but using a different topology, and if my new topology is stored in the directory somewhere/my_topology, then I should send the following command (for example for a md.com command): $GMXLIB=somewhere/my_topology md.com Right? And is it true that the by doing so, I will affect only this simulation, i.e. I will have changed the path to the topology only for this run, while for all the next ones the old path (/usr/share/gromacs/top) will be kept? Thank you, Nicola On Wed, May 21, 2014 at 11:37 AM, Chandan Choudhury iitd...@gmail.comwrote: Dear Nicola, Any number of users can use the top directory, with the choice of his/her force field. If anyone wants to edit the top files, then he can copy the top directory to somewhere and use the GMXLIB variable. You can use the GMXLIB environment variable, and point your top directory's path to it. For more details refer http://www.gromacs.org/Documentation/Terminology/Environment_Variables. Chandan On Wed, May 21, 2014 at 2:52 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear GROMACS user community, I have the following problem: I would like to let a simulation run on a computer where another simulation, prepared by another user, is already running; my simulation and the simulation of the other user need different topologies (I mean, for example, the files ffbonded.itp and ffnonbonded.itp files stored in /usr/share/gromacs/top/forcefield.ff are different; or, to make things more clear, let's suppose as a condition that user 1 needs to use charmm27.ff and user 2 gromos43a1.ff). Does anybody know of any solution where the number of computers is kept constant? What would happen, for example, if I would put my topology files inside my local working directory? Thank you very much in advance, Nicola -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Hi Tsierk, Ok. 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc -center -n index.ndx (centering all the frames on different targets Protein/DNA ecc ecc) (output system) 3) trjconv_mpi -s em.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect[or compact] (output System) I also tried, successively, the same procedure adding one step more: -pbc whole This last step was added before the step 1. But at the end I obtain the same result. Surely, I'm doing something wrong but I'm not understand what is wrong...:/ Thank you for your time. V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, May 21, 2014 11:58 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, Can you paste your exact workflow? Cheers, Tsjerk On Wed, May 21, 2014 at 9:53 AM, Vito Genna vito.ge...@iit.it wrote: Hi Tsierk, Hi tried your protocol without success. I have also tried different centering combination (on protein/DNA/Ligand/Protein+DNA/DNA+Ligand/Protein+ligand) and different flags combo (-pbc mol -ur compact/rect). I have added also the pbc whole before -pbc nojump but the result at the end is always the same, as shown in fig http://wikisend.com/download/185858/fig5.png The bonds are disappeared it's a god start but it is not enough to make measurements inside the catalytic pocket. I hope to find a solution with you and to write down a protocol for people which work whit ternary complexes. Thank you for your time. Best Regards V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, May 20, 2014 9:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, If the .tpr file is good, i.e. has everything assembled the way you want, then the first step is trjconv -pbc nojump. That will make sure that nothing gets split over PBC. Then center the protein in the box (trjconv -center), and subsequently put all molecules in the box (-pbc mol -ur compact/rect). Cheers, Tsjerk On Tue, May 20, 2014 at 7:51 PM, Vito Genna vito.ge...@iit.it wrote: Hi Tsjerk, Thank you for your email. No it is not broken. The structure is intact till the 20 ns of production phase. I have already used the .tpr (both md_0_1.tpr before, and then npt.tpr) obtaining the same result. Basically you are suggesting to fix the first frame of the production phase and use it as a reference point for the subsequent manipulations (-pbs nojump) of all TRJs? I'm going to do this attempt and I will keep you posted. Thanks again. Cheers V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, May 20, 2014 7:30 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, Was the structure already broken up when you solvated it? If not, which seems likely to me, then you can use that structure, or the .tpr from the EM in solvent, to remove jumps from the first frame of your run. After you unbroke the first frame, you can use that as reference for processing your trajectory with -pbc nojump. Hope it helps, Tsjerk On Tue, May 20, 2014 at 7:14 PM, Vito Genna
Re: [gmx-users] topology in local?
and grompp runs quite quickly, that's perfect, much less risky (for such a clumsy programmer like me!!) than changing the address $GMXLIB is pointing too (many won't agree on it, I guess ;) Thank you Justin!! Nicola On Wed, May 21, 2014 at 12:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/14, 5:22 AM, Nicola Staffolani wrote: Dear GROMACS user community, I have the following problem: I would like to let a simulation run on a computer where another simulation, prepared by another user, is already running; my simulation and the simulation of the other user need different topologies (I mean, for example, the files ffbonded.itp and ffnonbonded.itp files stored in /usr/share/gromacs/top/forcefield.ff are different; or, to make things more clear, let's suppose as a condition that user 1 needs to use charmm27.ff and user 2 gromos43a1.ff). Does anybody know of any solution where the number of computers is kept constant? What would happen, for example, if I would put my topology files inside my local working directory? Once grompp is invoked, the force field files in $GMXLIB (or anywhere else, for that matter) are irrelevant; everything mdrun needs is in the .tpr file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology in local?
On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? Sure. From what I have read about environment variableshttp://en.wikipedia.org/wiki/Environment_variable#Unix, if another simulation is already running on a computer and I want to launch my simulation but using a different topology, and if my new topology is stored in the directory somewhere/my_topology, then I should send the following command (for example for a md.com command): $GMXLIB=somewhere/my_topology md.com Right? And is it true that the by doing so, I will affect only this simulation, i.e. I will have changed the path to the topology only for this run, while for all the next ones the old path (/usr/share/gromacs/top) will be kept? I do not understand where your confusion lies. BTW, Gromacs works in the following way: 1. pdb2gmx generates the topolopy file (human readable). 2. grompp reads this topology and the structure file to generate a tpr (binary file). In the process of generating the tpr file, it reads the force field (FF) files. The location of the FF is taken from the GMXLIB variable. GMXLIB may point to any path of the computer where the FF is kept. 3. You can use this tpr file, to run your simulation to which every computer you want (gmx should be installed). If a simulation is already running, then your simulation would take more time to complete. Your tpr file will not be affected by the previous simulation. The same is also told by Justin. Thank you, Nicola -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology in local?
By the way, if I echo $GMXLIB, I can't see it, but GROMACS is working: is it OK? On Wed, May 21, 2014 at 12:27 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? From what I have read about environment variableshttp://en.wikipedia.org/wiki/Environment_variable#Unix, if another simulation is already running on a computer and I want to launch my simulation but using a different topology, and if my new topology is stored in the directory somewhere/my_topology, then I should send the following command (for example for a md.com command): $GMXLIB=somewhere/my_topology md.com Right? And is it true that the by doing so, I will affect only this simulation, i.e. I will have changed the path to the topology only for this run, while for all the next ones the old path (/usr/share/gromacs/top) will be kept? Thank you, Nicola On Wed, May 21, 2014 at 11:37 AM, Chandan Choudhury iitd...@gmail.comwrote: Dear Nicola, Any number of users can use the top directory, with the choice of his/her force field. If anyone wants to edit the top files, then he can copy the top directory to somewhere and use the GMXLIB variable. You can use the GMXLIB environment variable, and point your top directory's path to it. For more details refer http://www.gromacs.org/Documentation/Terminology/Environment_Variables. Chandan On Wed, May 21, 2014 at 2:52 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear GROMACS user community, I have the following problem: I would like to let a simulation run on a computer where another simulation, prepared by another user, is already running; my simulation and the simulation of the other user need different topologies (I mean, for example, the files ffbonded.itp and ffnonbonded.itp files stored in /usr/share/gromacs/top/forcefield.ff are different; or, to make things more clear, let's suppose as a condition that user 1 needs to use charmm27.ff and user 2 gromos43a1.ff). Does anybody know of any solution where the number of computers is kept constant? What would happen, for example, if I would put my topology files inside my local working directory? Thank you very much in advance, Nicola -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] High density after genbox
Thank you Mark, My Bad. Now fixed. Hope the simulations I did before were not affected, I had defined atomtypes with the correct mass in the .itp file used. Sujith On Wed, May 21, 2014 at 12:59 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Probably garbage in, garbage out. However you're measuring the density probably depends on share/top/atommass.dat, which relies on matching atom names to infer atom types and thus masses. If your atom names don't follow its assumptions... at least some tools warn about this in the output. Did the tool you were using not do so? Mark On Tue, May 20, 2014 at 12:50 PM, sujithkakkat . sujithk...@gmail.com wrote: Hello, I am working on a water-methane system with OPLSAA for methane and TIP4P/Ice for water. What I find strange is that after solvating the methane molecule with water (tip4p/ice) using the genbox routine, the density appears to be very high at 1661.04 (g/l) . The number of water molecules is normal for the box size, and therefore should give lower density values. After equilibration steps the density gets back to normal. Earlier , I ignored this problem and went ahead with the simulations, and the end results were found to be good. For eg, the solvation free energy of methane I calculated , was very close to reported values and also the value obtained in Justin's tutorial. Another test was simulating the tip4p/ice water , which gave results, for example the RDFs very close to the reported results. Could some one comment what is going on that gives the high density? Regards, Sujith. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Query regarding dssp plot
Dear Gromacs users, When I am using the DSSP program to generate the secondary structure changes of my protein (23 amino acids) and its mainchain, I am getting the results in the form of .eps file and using Ghostview, I visualized and saved in .jpeg format. But the figure looks blurred and I can not clearly see any secondary structure changes. Can anyone suggest me what and where I am doing the mistake and the possible solutions for this. I am attaching the figure with this mail for your reference. Thanking you, Regards Aditya. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology in local?
On 5/21/14, 7:34 AM, Nicola Staffolani wrote: By the way, if I echo $GMXLIB, I can't see it, but GROMACS is working: is it OK? Yes, that just suggests you've manually configured your path and library setup rather than sourcing GMXRC (which magically sorts everything out for you and sets environment variables). -Justin On Wed, May 21, 2014 at 12:27 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? From what I have read about environment variableshttp://en.wikipedia.org/wiki/Environment_variable#Unix, if another simulation is already running on a computer and I want to launch my simulation but using a different topology, and if my new topology is stored in the directory somewhere/my_topology, then I should send the following command (for example for a md.com command): $GMXLIB=somewhere/my_topology md.com Right? And is it true that the by doing so, I will affect only this simulation, i.e. I will have changed the path to the topology only for this run, while for all the next ones the old path (/usr/share/gromacs/top) will be kept? Thank you, Nicola On Wed, May 21, 2014 at 11:37 AM, Chandan Choudhury iitd...@gmail.comwrote: Dear Nicola, Any number of users can use the top directory, with the choice of his/her force field. If anyone wants to edit the top files, then he can copy the top directory to somewhere and use the GMXLIB variable. You can use the GMXLIB environment variable, and point your top directory's path to it. For more details refer http://www.gromacs.org/Documentation/Terminology/Environment_Variables. Chandan On Wed, May 21, 2014 at 2:52 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear GROMACS user community, I have the following problem: I would like to let a simulation run on a computer where another simulation, prepared by another user, is already running; my simulation and the simulation of the other user need different topologies (I mean, for example, the files ffbonded.itp and ffnonbonded.itp files stored in /usr/share/gromacs/top/forcefield.ff are different; or, to make things more clear, let's suppose as a condition that user 1 needs to use charmm27.ff and user 2 gromos43a1.ff). Does anybody know of any solution where the number of computers is kept constant? What would happen, for example, if I would put my topology files inside my local working directory? Thank you very much in advance, Nicola -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] grompp
On 5/21/14, 5:34 AM, Urszula Uciechowska wrote: Dear Gromacs users, I am new to Gromacs. I am trying to add ions to my protein system. After typing command: grompp -f grompp.mdp -c EcoLon6mer-sol.gro -p EcoLon6mer.top -o genion_input.tpr where the grompp.mdp contains: ; ions.mdp - used as input into grompp to generate ions.tpr ; 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 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) I am getting an error message: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# checking input for internal consistency... processing topology... Opening library file /software/local/Gromacs/4.5.3/Intel-ompi-fftw/share/gromacs/top/amber99.ff/forcefield.itp --- Program grompp, VERSION 4.0.7 Source code file: futil.c, line: 526 Fatal error: Library file ffnonbonded.itp not found in current dir nor in your GMXLIB path. --- Disturb the Peace of a John Q Citizen (Urban Dance Squad) How can I solve this problem? How can I add the path? The force field files should all be in the amber99.ff subdirectory of $GMXLIB. Is the file there? Does it have correct permissions (readable, at least)? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Query regarding dssp plot
Dear Justin, Thank you for the reply. I was using my 50 ns trajectory for generating the .xpm and .eps files. But when I tried the first 200 ps trajectory, I can see a clear image with helical content. I was wondering how to solve this because I have to use the whole 50 ns .tpr and .trr files. Please suggest me. Thanking you, Regards Aditya. On Wed, May 21, 2014 at 5:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/14, 7:56 AM, Aditya Padhi wrote: Dear Gromacs users, When I am using the DSSP program to generate the secondary structure changes of my protein (23 amino acids) and its mainchain, I am getting the results in the form of .eps file and using Ghostview, I visualized and saved in .jpeg format. But the figure looks blurred and I can not clearly see any secondary structure changes. Can anyone suggest me what and where I am doing the mistake and the possible solutions for this. I am attaching the figure with this mail for your reference. The list does not accept attachments. If you want to supply an image, upload it to a file-sharing server. If the image is simply distorted, that's where .m2p files are useful to alter the size properties of the matrix. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Aditya Kumar Padhi Ph.D Scholar School of Biological Sciences (SBS) Indian Institute of Technology Delhi New Delhi-110016, India Contact no:+91-9711539958 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Query regarding dssp plot
On 5/21/14, 8:13 AM, Aditya Padhi wrote: Dear Justin, Thank you for the reply. I was using my 50 ns trajectory for generating the .xpm and .eps files. But when I tried the first 200 ps trajectory, I can see a clear image with helical content. I was wondering how to solve this because I have to use the whole 50 ns .tpr and .trr files. Please suggest me. I already did: The list does not accept attachments. If you want to supply an image, upload it to a file-sharing server. If the image is simply distorted, that's where .m2p files are useful to alter the size properties of the matrix. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology in local?
and so how do I make GMXLIB point to somewhere else than /usr/share/gromacs/top? On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury iitd...@gmail.comwrote: On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? Sure. From what I have read about environment variableshttp://en.wikipedia.org/wiki/Environment_variable#Unix, if another simulation is already running on a computer and I want to launch my simulation but using a different topology, and if my new topology is stored in the directory somewhere/my_topology, then I should send the following command (for example for a md.com command): $GMXLIB=somewhere/my_topology md.com Right? And is it true that the by doing so, I will affect only this simulation, i.e. I will have changed the path to the topology only for this run, while for all the next ones the old path (/usr/share/gromacs/top) will be kept? I do not understand where your confusion lies. BTW, Gromacs works in the following way: 1. pdb2gmx generates the topolopy file (human readable). 2. grompp reads this topology and the structure file to generate a tpr (binary file). In the process of generating the tpr file, it reads the force field (FF) files. The location of the FF is taken from the GMXLIB variable. GMXLIB may point to any path of the computer where the FF is kept. 3. You can use this tpr file, to run your simulation to which every computer you want (gmx should be installed). If a simulation is already running, then your simulation would take more time to complete. Your tpr file will not be affected by the previous simulation. The same is also told by Justin. Thank you, Nicola -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] High density after genbox
The simulation uses the .itp contents, which goes into the .tpr. But in general the other tools either don't read that part of the .tpr, or you didn't give it to them in the first place (so they make do with atommass.dat). Mark On Wed, May 21, 2014 at 1:53 PM, sujithkakkat . sujithk...@gmail.comwrote: Thank you Mark, My Bad. Now fixed. Hope the simulations I did before were not affected, I had defined atomtypes with the correct mass in the .itp file used. Sujith On Wed, May 21, 2014 at 12:59 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Probably garbage in, garbage out. However you're measuring the density probably depends on share/top/atommass.dat, which relies on matching atom names to infer atom types and thus masses. If your atom names don't follow its assumptions... at least some tools warn about this in the output. Did the tool you were using not do so? Mark On Tue, May 20, 2014 at 12:50 PM, sujithkakkat . sujithk...@gmail.com wrote: Hello, I am working on a water-methane system with OPLSAA for methane and TIP4P/Ice for water. What I find strange is that after solvating the methane molecule with water (tip4p/ice) using the genbox routine, the density appears to be very high at 1661.04 (g/l) . The number of water molecules is normal for the box size, and therefore should give lower density values. After equilibration steps the density gets back to normal. Earlier , I ignored this problem and went ahead with the simulations, and the end results were found to be good. For eg, the solvation free energy of methane I calculated , was very close to reported values and also the value obtained in Justin's tutorial. Another test was simulating the tip4p/ice water , which gave results, for example the RDFs very close to the reported results. Could some one comment what is going on that gives the high density? Regards, Sujith. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology in local?
On 5/21/14, 8:38 AM, Nicola Staffolani wrote: and so how do I make GMXLIB point to somewhere else than /usr/share/gromacs/top? If Gromacs is installed in /usr/share/gromacs, that's where it should point. Otherwise, just override it by setting $GMXLIB in your shell however you like. Hopefully it won't break anything by doing that. -Justin On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury iitd...@gmail.comwrote: On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? Sure. From what I have read about environment variableshttp://en.wikipedia.org/wiki/Environment_variable#Unix, if another simulation is already running on a computer and I want to launch my simulation but using a different topology, and if my new topology is stored in the directory somewhere/my_topology, then I should send the following command (for example for a md.com command): $GMXLIB=somewhere/my_topology md.com Right? And is it true that the by doing so, I will affect only this simulation, i.e. I will have changed the path to the topology only for this run, while for all the next ones the old path (/usr/share/gromacs/top) will be kept? I do not understand where your confusion lies. BTW, Gromacs works in the following way: 1. pdb2gmx generates the topolopy file (human readable). 2. grompp reads this topology and the structure file to generate a tpr (binary file). In the process of generating the tpr file, it reads the force field (FF) files. The location of the FF is taken from the GMXLIB variable. GMXLIB may point to any path of the computer where the FF is kept. 3. You can use this tpr file, to run your simulation to which every computer you want (gmx should be installed). If a simulation is already running, then your simulation would take more time to complete. Your tpr file will not be affected by the previous simulation. The same is also told by Justin. Thank you, Nicola -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology in local?
just to improve my knowledge in programming: and I can override it by typing: GMXLIB=address_of_the_new_topology_in_my_computer right? But in that case, if I first open a child shell, then the change will be effective only there, and as soon as I come back to the parent shell, GMXLIB will be pointing to the old /usr/share/... address, right? Thank you Justin! PS I do not think I will try to override it anyway ;) And yes, I manually installed GROMACS because I didn't know I could do it by just using Ubuntu Software Center... On Wed, May 21, 2014 at 2:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/14, 8:38 AM, Nicola Staffolani wrote: and so how do I make GMXLIB point to somewhere else than /usr/share/gromacs/top? If Gromacs is installed in /usr/share/gromacs, that's where it should point. Otherwise, just override it by setting $GMXLIB in your shell however you like. Hopefully it won't break anything by doing that. -Justin On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury iitd...@gmail.com wrote: On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? Sure. From what I have read about environment variableshttp://en.wikipedia.org/wiki/Environment_variable#Unix, if another simulation is already running on a computer and I want to launch my simulation but using a different topology, and if my new topology is stored in the directory somewhere/my_topology, then I should send the following command (for example for a md.com command): $GMXLIB=somewhere/my_topology md.com Right? And is it true that the by doing so, I will affect only this simulation, i.e. I will have changed the path to the topology only for this run, while for all the next ones the old path (/usr/share/gromacs/top) will be kept? I do not understand where your confusion lies. BTW, Gromacs works in the following way: 1. pdb2gmx generates the topolopy file (human readable). 2. grompp reads this topology and the structure file to generate a tpr (binary file). In the process of generating the tpr file, it reads the force field (FF) files. The location of the FF is taken from the GMXLIB variable. GMXLIB may point to any path of the computer where the FF is kept. 3. You can use this tpr file, to run your simulation to which every computer you want (gmx should be installed). If a simulation is already running, then your simulation would take more time to complete. Your tpr file will not be affected by the previous simulation. The same is also told by Justin. Thank you, Nicola -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. Thanks again. V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, May 21, 2014 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: Hi Tsierk, Ok. 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc -center -n index.ndx (centering all the frames on different targets Protein/DNA ecc ecc) (output system) 3) trjconv_mpi -s em.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect[or compact] (output System) I also tried, successively, the same procedure adding one step more: -pbc whole This last step was added before the step 1. But at the end I obtain the same result. Surely, I'm doing something wrong but I'm not understand what is wrong...:/ Thank you for your time. V -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology in local?
On 5/21/14, 9:06 AM, Nicola Staffolani wrote: just to improve my knowledge in programming: and I can override it by typing: GMXLIB=address_of_the_new_topology_in_my_computer right? The details depend on your shell. For csh you need setenv, for bash you need export, etc. Quotes shouldn't be necessary, e.g.: export GMXLIB=/home/justin/software/gromacs/custom/share/top But in that case, if I first open a child shell, then the change will be effective only there, and as soon as I come back to the parent shell, GMXLIB will be pointing to the old /usr/share/... address, right? Thank you Justin! Any new shell you open will need the environment variable to be set again; if it's something you need often (or always) set it in .bashrc, .cshrc, etc. -Justin PS I do not think I will try to override it anyway ;) And yes, I manually installed GROMACS because I didn't know I could do it by just using Ubuntu Software Center... On Wed, May 21, 2014 at 2:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/14, 8:38 AM, Nicola Staffolani wrote: and so how do I make GMXLIB point to somewhere else than /usr/share/gromacs/top? If Gromacs is installed in /usr/share/gromacs, that's where it should point. Otherwise, just override it by setting $GMXLIB in your shell however you like. Hopefully it won't break anything by doing that. -Justin On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury iitd...@gmail.com wrote: On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? Sure. From what I have read about environment variableshttp://en.wikipedia.org/wiki/Environment_variable#Unix, if another simulation is already running on a computer and I want to launch my simulation but using a different topology, and if my new topology is stored in the directory somewhere/my_topology, then I should send the following command (for example for a md.com command): $GMXLIB=somewhere/my_topology md.com Right? And is it true that the by doing so, I will affect only this simulation, i.e. I will have changed the path to the topology only for this run, while for all the next ones the old path (/usr/share/gromacs/top) will be kept? I do not understand where your confusion lies. BTW, Gromacs works in the following way: 1. pdb2gmx generates the topolopy file (human readable). 2. grompp reads this topology and the structure file to generate a tpr (binary file). In the process of generating the tpr file, it reads the force field (FF) files. The location of the FF is taken from the GMXLIB variable. GMXLIB may point to any path of the computer where the FF is kept. 3. You can use this tpr file, to run your simulation to which every computer you want (gmx should be installed). If a simulation is already running, then your simulation would take more time to complete. Your tpr file will not be affected by the previous simulation. The same is also told by Justin. Thank you, Nicola -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
On Wed, May 21, 2014 at 6:37 PM, Vito Genna vito.ge...@iit.it wrote: Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. It seems that the tpr you are supplying has PBC in it. I assume the first tpr should be generated from PBC free structure. That is the understanding I had. Correct me if I am wrong. Chandan Thanks again. V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, May 21, 2014 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: Hi Tsierk, Ok. 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc -center -n index.ndx (centering all the frames on different targets Protein/DNA ecc ecc) (output system) 3) trjconv_mpi -s em.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect[or compact] (output System) I also tried, successively, the same procedure adding one step more: - pbc whole This last step was added before the step 1. But at the end I obtain the same result. Surely, I'm doing something wrong but I'm not understand what is wrong...:/ Thank you for your time. V -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cannot Generate CHARMM36 Topology for POPC with Virtual Sites
Dear Justin, I am facing the same problem and only difference is that I am using POPE lipids. I am using GROMACS 4.6.5 and error exists for in built CHARMM27 and CHARMM36 march release. Parameters are missing for following atomtypes. MNH3 CTL2 MCH3 CTL2 I have gone through the ff files and I found something as following. The section of ffbonded.itp file of CHARMM36 is, --- [ constrainttypes ] ; this section is copied from OPLS. In theory we could recalculate ; optimal geometries from charmm values, but since pratical equilibrium ; geometries do not correspond exactly to these values anyway it is not ; worth the effort... #ifdef HEAVY_H ; account for larger inertia with heavy hydrogens ; constraints for the rigid NH3 groups MNH3 CT1 20.191406 MNH3 CT2 20.191406 MNH3 CT3 20.191406 MNH3MNH3 20.165238 ; constraints for rigid ch3 MCH3 CT1 20.206892 MCH3 CT2 20.206000 MCH3 CT3 20.206179 MCH3MCH3 20.185689 MCH3 S 20.25 #else ; no heavy hydrogens. ; constraints for the rigid NH3 groups MNH3 CT1 20.159603 MNH3 CT2 20.159603 MNH3 CT3 20.159603 MNH3MNH3 20.082619 ; constraints for rigid ch3 MCH3 CT1 20.168122 MCH3 CT2 20.167162 MCH3 CT3 20.167354 MCH3MCH3 20.093582 MCH3 S 20.195314 #endif --- In above section we can see that the parameters for CT2 is present which is aliphatic sp3 C for CH2 and it belongs to proteins MNH3 CT2 20.191406 MCH3 CT2 20.206000 The atomtype CTL2 is for carbon of methylene group (-CH2-) and it belong to lipid. According to atom type definitions, both carbons are same but belongs to different residues. I have not tested by adding the values (will be done soon). So, the question is that can I use CT2 parameters for CTL2 atomtype? Thank you -Jignesh From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Tuesday, April 08, 2014 9:37 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Cannot Generate CHARMM36 Topology for POPC with Virtual Sites On 4/8/14, 12:45 PM, Chris Ing wrote: I'm trying to build a charmm36.ff topology file for a POPC with virtual sites. In GROMACS 4.5.5 and 4.6.3 (with the most recent CHARMM36 March 2014), when I run: pdb2gmx -f POPC.pdb -o POPC.gro -p POPC.top -i POPC.posre -vsite hydrogen grompp -f empty.mdp -c POPC.gro -p POPC.top -o test.tpr I get multiple constraint errors: ERROR 1 [file POPC.top, line 311]: No default Constr. No Conn. types Which is due to the lack of two constraints not in ffbonded.itp: MCH3 NTL MCH3 CTL2 MCH3 is the virtual site of a CH3 group, and NTL refers to the choline nitrogen in the POPC headgroup and CTL2, in this case, is the carbon closest to the CH3 group on the POPC tail. The same question was asked in the gmx-users thread amber99sb_virtual site lipids dopc MCH3_N constraint types by Song Ke, where the reply from Erik Marklund was to manually add this value from bond lengths, center of mass for the group and the moment of inertia.. In lieu of wiping an inch of dust off my classical mechanics textbook, I wondered if I could copy some additional constraint values from the OPLS ffbonded.itp file. The charmm36.ff ffbonded.itp file states that the constrainttypes section is copied directly from OPLS (the restraint values are slightly adjusted?). Yet, many entries were not copied from OPLS to CHARMM36: OPLS: MNH3 CT_2 20.158255 MNH3 MNH3 20.080236 MCH3A C 20.166040 MCH3A C_2 20.166040 MCH3ACW 20.164312 MCH3ACV 20.164312 MCH3ACS 20.163448 MCH3ACA 20.164888 MCH3ACB 20.164888 MCH3A N 20.159040 MCH3A S 20.193874 MCH3A MCH3A 20.092160 MCH3BCT 20.167031 MCH3B CT_2 20.167031 MCH3B CT_3 20.167031 MCH3BCO 20.167031 MCH3B MCH3B 20.091456 CHARMM36: MNH3 CT3 20.159603 MNH3MNH3 20.082619 MCH3 CT1 20.168122 MCH3 CT2 20.167162 MCH3 CT3 20.167354 MCH3 S 20.195314 MCH3MCH3 20.093582 Would it be acceptable to use these OPLS constraint values in CHARMM36 to resolve my problem?: MCH3A N 20.159040 MCH3BCT 20.167031 Thanks gmx-users/Justin Lemkul! For what it's worth, we have done exactly zero testing with virtual sites. The sections of text you are referring to were copied basically verbatim from what was distributed as charmm27.ff in Gromacs prior to our creation of charmm36.ff. I don't know if that's of any use, but please consider it at least a strong disclaimer :) -Chris P.S. I had
Re: [gmx-users] topology in local?
On Wed, May 21, 2014 at 12:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/14, 5:22 AM, Nicola Staffolani wrote: Dear GROMACS user community, I have the following problem: I would like to let a simulation run on a computer where another simulation, prepared by another user, is already running; my simulation and the simulation of the other user need different topologies (I mean, for example, the files ffbonded.itp and ffnonbonded.itp files stored in /usr/share/gromacs/top/forcefield.ff are different; or, to make things more clear, let's suppose as a condition that user 1 needs to use charmm27.ff and user 2 gromos43a1.ff). Does anybody know of any solution where the number of computers is kept constant? What would happen, for example, if I would put my topology files inside my local working directory? Once grompp is invoked, the force field files in $GMXLIB (or anywhere else, for that matter) are irrelevant; everything mdrun needs is in the .tpr file. /nitpick If using tabulated interactions, those need to be supplied to mdrun as well. But we'd like to (find time to) put them into the .tpr, too. The objective is that you should be able to construct the .tpr on your local machine and have it run the same on any machine in the world. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] entropy vs time plot
Dear Sir,
Thanks for the piece of script.
Bit modification and it works superbly.
thanks,
Tarak
On Wed, May 21, 2014 at 1:23 PM, David van der Spoel
sp...@xray.bmc.uu.sewrote:
On 2014-05-21 06:54, tarak karmakar wrote:
Hi Tsjerk,
Thanks for the quick reply.
I did the following
g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v
eigenvec.trr -av average.pdb -b 0 -e 1
g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 1
What I want to plot is similar to this.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/
Is there any flag for this?
I've checked g_covar -h and g_anaeig -h but didn't get the proper way.
You need to run a
for($N=1000; ($N=1); $N+= 100) {
g_covar -e $N
g_anaeig
grep S from standard out and save it
}
Thanks,
Tarak
On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi Tarak,
You will have to use -b/-e to set the start and end times.
Cheers,
Tsjerk
On Tue, May 20, 2014 at 12:18 PM, tarak karmakar tarak20...@gmail.com
wrote:
Dear All,
Could anyone tell me how to plot configurational entropy as a function
of
simulation time?
Do I need to manually specify the -dt(say after each 1 ns) during the
g_covar and then do g_anaeig in each of the step?
thanks,
Tarak
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[gmx-users] Multi-node GPU runs crashing with a fork() warning
Hey Folks, I'm attempting to run simulations on a multi-node gpu cluster and my simulations are crashing after flagging a open-mpi fork() warning: *--* *An MPI process has executed an operation involving a call to the* *fork() system call to create a child process. Open MPI is currently* *operating in a condition that could result in memory corruption or* *other system errors; your MPI job may hang, crash, or produce silent* *data corruption. The use of fork() (or system() or other calls that* *create child processes) is strongly discouraged.* *The process that invoked fork was:* * Local host: lngpu019 (PID 11549)* * MPI_COMM_WORLD rank: 18* *If you are *absolutely sure* that your application will successfully* *and correctly survive a call to fork(), you may disable this warning* *by setting the mpi_warn_on_fork MCA parameter to 0.* *--* I saw a similar mailing-list post about this sort of issue from September 2013, but the thread had no resolution. - Each node of our cluster has has 12 intel cores and 6 NVIDIA Tesla C2050 GPU's. - we call: mpirun -machinefile nodes.txt -npernode 6 mdrun_mpi - I compiled GROMACS on one of the compute nodes with the C2050's. We also have a few nodes with newer K20 NVIDIA GPU's. When we compile GROMACS on these nodes we can run the code across multiple nodes and GPU's without any errors. I don't know if the fork() error is directly related to the crash or not; or if there might be obscure, device specific object files outside my build directory, that I should delete. Any insight you folks could provide to help me solve this issue would be appreciated. Thanks, -- Thomas O'Connor Graduate Research Assistant MCS IGERT Fellow Department of Physics Astronomy The Johns Hopkins University 3701 San Martin Drive Baltimore, MD 21218*tocon...@jhu.edu tocon...@jhu.edu*410.516.8587 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
That doesn't make sense..., sorry. Cheers, Tsjerk On May 21, 2014 6:40 PM, Chandan Choudhury iitd...@gmail.com wrote: On Wed, May 21, 2014 at 6:37 PM, Vito Genna vito.ge...@iit.it wrote: Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. It seems that the tpr you are supplying has PBC in it. I assume the first tpr should be generated from PBC free structure. That is the understanding I had. Correct me if I am wrong. Chandan Thanks again. V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, May 21, 2014 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: Hi Tsierk, Ok. 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc -center -n index.ndx (centering all the frames on different targets Protein/DNA ecc ecc) (output system) 3) trjconv_mpi -s em.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect[or compact] (output System) I also tried, successively, the same procedure adding one step more: - pbc whole This last step was added before the step 1. But at the end I obtain the same result. Surely, I'm doing something wrong but I'm not understand what is wrong...:/ Thank you for your time. V -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Would suggest that each time you try a different workflow, do so in a new subdirectory and copy the required files into there. That way you ensure are using the files you think that you are. Will help those assisting to then post an image of the coordinate files at each step of the work flow, to see how things are changing, or not. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Vito Genna Sent: Wednesday, 21 May 2014 11:07 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. Thanks again. V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy --- -- The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, May 21, 2014 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: Hi Tsierk, Ok. 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc - center -n index.ndx (centering all the frames on different targets Protein/DNA ecc ecc) (output system) 3) trjconv_mpi -s em.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect[or compact] (output System) I also tried, successively, the same procedure adding one step more: -pbc whole This last step was added before the step 1. But at the end I obtain the same result. Surely, I'm doing something wrong but I'm not understand what is wrong...:/ Thank you for your time. V -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Multi-node GPU runs crashing with a fork() warning
Hi, Sounds like an MPI or MPI+CUDA issue. Does mdrun run if you use a single GPU? How about two? Btw, unless you have some rather exotic setup, you won't be able to get much improvement from using more than three, at most four GPUs per node - you need CPU cores to match them (and a large system to deed the GPUs and scale). Multi runs could work well, though. Cheers, -- Szilárd On Wed, May 21, 2014 at 6:29 PM, Thomas C. O'Connor tocon...@jhu.edu wrote: Hey Folks, I'm attempting to run simulations on a multi-node gpu cluster and my simulations are crashing after flagging a open-mpi fork() warning: *--* *An MPI process has executed an operation involving a call to the* *fork() system call to create a child process. Open MPI is currently* *operating in a condition that could result in memory corruption or* *other system errors; your MPI job may hang, crash, or produce silent* *data corruption. The use of fork() (or system() or other calls that* *create child processes) is strongly discouraged.* *The process that invoked fork was:* * Local host: lngpu019 (PID 11549)* * MPI_COMM_WORLD rank: 18* *If you are *absolutely sure* that your application will successfully* *and correctly survive a call to fork(), you may disable this warning* *by setting the mpi_warn_on_fork MCA parameter to 0.* *--* I saw a similar mailing-list post about this sort of issue from September 2013, but the thread had no resolution. - Each node of our cluster has has 12 intel cores and 6 NVIDIA Tesla C2050 GPU's. - we call: mpirun -machinefile nodes.txt -npernode 6 mdrun_mpi - I compiled GROMACS on one of the compute nodes with the C2050's. We also have a few nodes with newer K20 NVIDIA GPU's. When we compile GROMACS on these nodes we can run the code across multiple nodes and GPU's without any errors. I don't know if the fork() error is directly related to the crash or not; or if there might be obscure, device specific object files outside my build directory, that I should delete. Any insight you folks could provide to help me solve this issue would be appreciated. Thanks, -- Thomas O'Connor Graduate Research Assistant MCS IGERT Fellow Department of Physics Astronomy The Johns Hopkins University 3701 San Martin Drive Baltimore, MD 21218*tocon...@jhu.edu tocon...@jhu.edu*410.516.8587 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cannot Generate CHARMM36 Topology for POPC with Virtual Sites
On 5/21/14, 11:27 AM, Prajapati, Jigneshkumar Dahyabhai wrote: Dear Justin, I am facing the same problem and only difference is that I am using POPE lipids. I am using GROMACS 4.6.5 and error exists for in built CHARMM27 and CHARMM36 march release. Parameters are missing for following atomtypes. MNH3 CTL2 MCH3 CTL2 I have gone through the ff files and I found something as following. The section of ffbonded.itp file of CHARMM36 is, --- [ constrainttypes ] ; this section is copied from OPLS. In theory we could recalculate ; optimal geometries from charmm values, but since pratical equilibrium ; geometries do not correspond exactly to these values anyway it is not ; worth the effort... #ifdef HEAVY_H ; account for larger inertia with heavy hydrogens ; constraints for the rigid NH3 groups MNH3 CT1 20.191406 MNH3 CT2 20.191406 MNH3 CT3 20.191406 MNH3MNH3 20.165238 ; constraints for rigid ch3 MCH3 CT1 20.206892 MCH3 CT2 20.206000 MCH3 CT3 20.206179 MCH3MCH3 20.185689 MCH3 S 20.25 #else ; no heavy hydrogens. ; constraints for the rigid NH3 groups MNH3 CT1 20.159603 MNH3 CT2 20.159603 MNH3 CT3 20.159603 MNH3MNH3 20.082619 ; constraints for rigid ch3 MCH3 CT1 20.168122 MCH3 CT2 20.167162 MCH3 CT3 20.167354 MCH3MCH3 20.093582 MCH3 S 20.195314 #endif --- In above section we can see that the parameters for CT2 is present which is aliphatic sp3 C for CH2 and it belongs to proteins MNH3 CT2 20.191406 MCH3 CT2 20.206000 The atomtype CTL2 is for carbon of methylene group (-CH2-) and it belong to lipid. According to atom type definitions, both carbons are same but belongs to different residues. I have not tested by adding the values (will be done soon). So, the question is that can I use CT2 parameters for CTL2 atomtype? I have never tried it since I've never had reason to. If you've got tests underway, please report back on how they turn out, either to the list or directly to me. We will probably be putting out a new release of the CHARMM36 FF sometime soon, so it would be good to include little fixes like these. -Justin Thank you -Jignesh From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Tuesday, April 08, 2014 9:37 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Cannot Generate CHARMM36 Topology for POPC with Virtual Sites On 4/8/14, 12:45 PM, Chris Ing wrote: I'm trying to build a charmm36.ff topology file for a POPC with virtual sites. In GROMACS 4.5.5 and 4.6.3 (with the most recent CHARMM36 March 2014), when I run: pdb2gmx -f POPC.pdb -o POPC.gro -p POPC.top -i POPC.posre -vsite hydrogen grompp -f empty.mdp -c POPC.gro -p POPC.top -o test.tpr I get multiple constraint errors: ERROR 1 [file POPC.top, line 311]: No default Constr. No Conn. types Which is due to the lack of two constraints not in ffbonded.itp: MCH3 NTL MCH3 CTL2 MCH3 is the virtual site of a CH3 group, and NTL refers to the choline nitrogen in the POPC headgroup and CTL2, in this case, is the carbon closest to the CH3 group on the POPC tail. The same question was asked in the gmx-users thread amber99sb_virtual site lipids dopc MCH3_N constraint types by Song Ke, where the reply from Erik Marklund was to manually add this value from bond lengths, center of mass for the group and the moment of inertia.. In lieu of wiping an inch of dust off my classical mechanics textbook, I wondered if I could copy some additional constraint values from the OPLS ffbonded.itp file. The charmm36.ff ffbonded.itp file states that the constrainttypes section is copied directly from OPLS (the restraint values are slightly adjusted?). Yet, many entries were not copied from OPLS to CHARMM36: OPLS: MNH3 CT_2 20.158255 MNH3 MNH3 20.080236 MCH3A C 20.166040 MCH3A C_2 20.166040 MCH3ACW 20.164312 MCH3ACV 20.164312 MCH3ACS 20.163448 MCH3ACA 20.164888 MCH3ACB 20.164888 MCH3A N 20.159040 MCH3A S 20.193874 MCH3A MCH3A 20.092160 MCH3BCT 20.167031 MCH3B CT_2 20.167031 MCH3B CT_3 20.167031 MCH3BCO 20.167031 MCH3B MCH3B 20.091456 CHARMM36: MNH3 CT3 20.159603 MNH3MNH3 20.082619 MCH3 CT1 20.168122 MCH3 CT2 20.167162 MCH3 CT3 20.167354 MCH3 S 20.195314 MCH3MCH3 20.093582 Would it be acceptable to use these OPLS constraint values in CHARMM36 to resolve my problem?: MCH3A N 20.159040 MCH3BCT 20.167031 Thanks gmx-users/Justin Lemkul! For what it's worth, we
[gmx-users] Nanoparticle topology
Dear sir, I need to simulate gold nanoparticles (*NP*) interaction with some ligands (drugs). I can get ligand topology via ATB/ Prodrug server, but I can't get nanoparticle topology. Is there any external tools for *NP* modelling and topology generation.? Any other modifications to simulate metal atoms via GROMACS.? Thanks in advance -- Guhan.KA -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] about exchange replica with replicas 140
Dear gromacs user: I have encounter a problem when used HPC(high performance computer) to run replica exchange. I find that when I used replica over 128, it will not work, while under 128 , it is ok, even when I used cores much more than 128(several cores for one replica). The version I used is gromacs-4.6.2-double-intel. Hope for you help. Best regards, Haiping Zhang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] about exchange replica with replicas 140
On 5/21/14, 10:53 PM, #ZHANG HAIPING# wrote: Dear gromacs user: I have encounter a problem when used HPC(high performance computer) to run replica exchange. I find that when I used replica over 128, it will not work, while under 128 , it is ok, even when I used cores much more than 128(several cores for one replica). The version I used is gromacs-4.6.2-double-intel. Hope for you help. You need to provide more information. Specifically, what commands are you issuing? What does will not work mean? Is there a specific error you are getting? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] lifetime of hydrogen bond of bulk water too large
I mean't to type that the expected value should be around 0.27ps but I am getting 2 to 3 ps from my simulations. The autocorrelation function decays to 0. Is there something I am missing? Any insight would be appreciated. Thanks. Emvia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] entropy vs time plot
Yah but youll have to smooth it, mean wise, or beter averidge several runs. qtiplot or equivalent will work (even MS Excell if you have the added mean determination formulas). Stephan Watkins Gesendet:Mittwoch, 21. Mai 2014 um 06:54 Uhr Von:tarak karmakar tarak20...@gmail.com An:Discussion list for GROMACS users gmx-us...@gromacs.org Betreff:Re: [gmx-users] entropy vs time plot Hi Tsjerk, Thanks for the quick reply. I did the following g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v eigenvec.trr -av average.pdb -b 0 -e 1 g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 1 What I want to plot is similar to this. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/ Is there any flag for this? Ive checked g_covar -h and g_anaeig -h but didnt get the proper way. Thanks, Tarak On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Tarak, You will have to use -b/-e to set the start and end times. Cheers, Tsjerk On Tue, May 20, 2014 at 12:18 PM, tarak karmakar tarak20...@gmail.com wrote: Dear All, Could anyone tell me how to plot configurational entropy as a function of simulation time? Do I need to manually specify the -dt(say after each 1 ns) during the g_covar and then do g_anaeig in each of the step? thanks, Tarak -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] 答复: about exchange replica with replicas 140
Dear Justin: The scripts I used is as follow: ## Set job parameters ## Job Name #BSUB -J OpenMPI ## Queue Name #BSUB -q medium_priority ## Output and Input Errors #BSUB -o job%J.out #BSUB -e job%J.err ## Specify walltime in HH:MM #BSUB -W 60:00 ## 16 Processors per Host #BSUB -R span[ptile=16] ## Requesting for 32 cores #BSUB -n 140 # Need to make our own machinefile MACHINEFILE=mymacs.$LSB_JOBID for i in `echo $LSB_HOSTS` do echo $i done $MACHINEFILE ## load module enviroement module load openmpi-1.6.5-intel-v12.1.5 module load intel-12.1.5 ## Run mpi program cd /gpfs/home/hzhang020/REMD/remdrun/scratch /usr/local/RH6_apps/openmpi-1.6.5-intel-v12.1.5/bin/mpirun --bind-to-core --report-bindings -np 140 -machinefile $MACHINEFILE /usr/local/RH6_apps/gromacs-4.6.2-double-intel/bin/mdrun_mpi_d -s prefix_.tpr -multi 140 -replex 3000 There was not obvious error information, just have the output file size is always 0. After long time, I kill it myself. NOTE: The load imbalance in PME FFT and solve is 384%. For optimal PME load balancing PME grid_x (1728) and grid_y (1728) should be divisible by #PME_nodes_x (2) and PME grid_y (1728) and grid_z (1728) should be divisible by #PME_nodes_y (1) NOTE: The load imbalance in PME FFT and solve is 384%. For optimal PME load balancing PME grid_x (1728) and grid_y (1728) should be divisible by #PME_nodes_x (2) and PME grid_y (1728) and grid_z (1728) should be divisible by #PME_nodes_y (1) -- WARNING: A process refused to die! Host: comp094 PID: 6751 This process may still be running and/or consuming resources. -- -- mpirun noticed that process rank 273 with PID 30914 on node comp122 exited on signal 9 (Killed). -- 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul jalem...@vt.edu 发送时间: 2014年5月22日 10:57 收件人: gmx-us...@gromacs.org 主题: Re: [gmx-users] about exchange replica with replicas 140 On 5/21/14, 10:53 PM, #ZHANG HAIPING# wrote: Dear gromacs user: I have encounter a problem when used HPC(high performance computer) to run replica exchange. I find that when I used replica over 128, it will not work, while under 128 , it is ok, even when I used cores much more than 128(several cores for one replica). The version I used is gromacs-4.6.2-double-intel. Hope for you help. You need to provide more information. Specifically, what commands are you issuing? What does will not work mean? Is there a specific error you are getting? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
