[gmx-users] g_rms and g_rmsdist on initial structure
Hi, For example, I have a A.pdb as a initial structure file. And I just used pdb2gmx on it to generate another B.pdb file with GROMOS96 43a1 as its force filed. Then I select C-alpha atoms to calculate RMSD. echo 3 | g_rms -f B.pdb -s A.pdb I suppose the RMSD value should be 0, but the value is high to about 0.5nm. Can someone explain for me? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Is openmp necessary?
Hi, For mdrun, the option -nt means Number of threads to start (0 is guess). Is this option executed by openmp? I used this option every time. But today my technology stuff told me that we don't have openmp installed in our computer. It make me confused. Why can I compile and run mdrun -nt 12 before? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Is openmp necessary?
Hi Mark, Thank you for your reply. I understand now. Sincerely yours, Hsin-Lin I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial displacement. this will give rise to a non-realistic MSD. is g_msd intelligent enough to avoid this artificial displacement? Yes it is. Not sure about g_msd, but you can take care of it yourself with a workflow derived from the information here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] part number in extending simulation
Hi,
Is part number in extending simulation in ver.4.5.4 cancelled?
Below is my shell script,
#!/bin/bash
a=/stathome/jiangsl/simulation/gromacs/d1GUJ_AB/4md
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.5.4/bin/mdrun \
-nt 12 \
-s ${a}/md100ns.tpr \
-o ${a}/md100ns.trr \
-e ${a}/md100ns.edr \
-g ${a}/md100ns.log \
-c ${a}/md100ns.gro \
-cpo ${a}/md100ns.cpt \
-cpi ${a}/md50ns.cpt
#
In GROMACS ver.4.0.5, if I use this script I'll get files such as
md100ns.part002.trr,
md100ns.part002.gro, md100ns.part002.edr, and md100ns.part002.log.
But in ver.4.5.4 I only get md100ns.trr, md100ns.gro, md100ns.edr, and
md100ns.log.
So, is the function of part number in extending simulation in ver.4.5.4
cancelled?
Hsin-Lin
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[gmx-users] part number in extending simulation
Hi Flo, Thank you for reply. I got it. But as you see I also indicate the new names for output files. Do I get correct result in this kind of situation? Or I need to rerun it with -noappend Sincerely yours, Hsin-Lin Hi, check the standard options of mdrun with the help flag -h of version 4.5.4 and below. You will realize, that the standard append behaviour changed from no to yes. Hence if you start from a checkpoint and files are already present in the working directory the integration results will be appended. Flo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] part number in extending simulation
I am not sure, but I assume if you set new names, new files will be created. The checkpoint input files contains important information about your coordinates, velocities, states of random number generators for the NH coupling That is the reason, why it is necessary for a continuous extension of your run. The results should not depend on the append option, only the number of resulting trajectories is affected. The suffix part??? will just arise if the files are already present and you use -noappend. Now you will end up with two trajectories I assume: * md50ns, * md100ns, which are indistinguishable from a single continuous 100ns run and I think that is what you want, isn't it ? /Flo Thank you. I'm not sure,too. Exactly mdrun create md100ns.trr for me, but I'm not sure if any thing is right in the file. So I added -noappend to rerun it again and this result will be correct without doubt. By the way, md100ns.trr here mean from 50ns to 100ns. I just don't want the new run append to md50ns.trr to make me confused. Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] increasing cut-off and PME grid spacing
Hi Justin, I understand now. The vector of box changed from 5.8 to 44 after the short MD for equilibrium. I don't know what happened during equilibrium. But that is belong to the other question now. Thank you very much for your reply. Sincerely yours, Hsin-LIn Hsin-Lin Chiang wrote: Hi, Justin Sorry for the unclear message. My box vector in .gro file are 44.22834 #160;44.22834 #160;44.22834 and the number of atoms is 20171 You've set an unreasonably large box, as I expected. #160;The box should be set in nm, not Angstrom. #160;20171 atoms is a fairly small system, and in effect what you've created is a protein in a droplet of water, surrounded by vacuum. #160;90% of the work done by PME will be to calculate a grid of nothing. The output of grompp is shown below, I don't know if it is enough and I'm sorry I don't know how should I do after you reply. Could you please give me more messages in detail? The solution is to set a correct box, unless your objective is to simulate a droplet, in which case you have no choice but to take the performance loss inherent to using PME. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] increasing cut-off and PME grid spacing
Hi, I want to run mdrun -nt 12 on our cluster. When I execute, grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p ../initial/insulin.top -n ../initial/index.ndx I got the message, Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 1 [file test.mdp]: #160; The optimal PME mesh load for parallel simulations is below 0.5 #160; and for highly parallel simulations between 0.25 and 0.33, #160; for higher performance, increase the cut-off and the PME grid spacing Then I changed my mdp to get Estimate for the relative computational load of the PME mesh part: 0.20 Belos is my new mdp file I change rlist, rcoulumb, and rvdw from 1 to 12 and fourierspacing from 0.2 to 2 to get the lower relative computational load. I'm afraid these extreme high value caused some bad effect. title#160;#160;#160;#160;#160;#160;#160; = ttt cpp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; /lib/cpp constraints#160;#160;#160;#160;#160;#160;#160;#160; =#160; hbonds ;define#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; -DFLEX_SPC integrator#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; md emtol#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 100.0 emstep#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.005 dt#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.002#160;#160;#160; ; ps ! nsteps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 2500#160; ; total 50 ns nstcomm#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 5000 nstxout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 5000 nstvout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 5000 nstfout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 5000 nstlog#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 5000 nstenergy#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 5000 nstlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 10 ns_type#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; grid rlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 12 rcoulomb#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 12 rvdw#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 12 coulombtype#160;#160;#160;#160;#160;#160;#160;#160; =#160; PME fourierspacing#160;#160;#160;#160;#160; =#160; 2 pme_order#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 6 optimize_fft#160;#160;#160;#160;#160;#160;#160; =#160; yes Tcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; v-rescale tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; Protein Non-Protein ;tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.1#160; 0.1 tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.2 0.2 ref_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 300 300 energygrps#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; A-chain B-chain SOL NA Pcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; berendsen Pcoupltype#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; isotropic ;tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.1 tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.25 compressibility#160;#160;#160;#160; =#160; 5.4e-5 ref_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 1.0 gen_vel#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; yes gen_temp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 300 gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 173529 Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] increasing cut-off and PME grid spacing
Sorry for the confusing symbol. I tried to change it in this new mail. Hi, I want to run mdrun -nt 12 on our cluster. When I execute, grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p ../initial/insulin.top -n ../initial/index.ndx I got the message, Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 1 [file test.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Then I changed my mdp to get Estimate for the relative computational load of the PME mesh part: 0.20 Belos is my new mdp file I change rlist, rcoulumb, and rvdw from 1 to 12 and fourierspacing from 0.2 to 2 to get the lower relative computational load. I'm afraid these extreme high value caused some bad effect. title = ttt cpp = /lib/cpp constraints = hbonds ;define = -DFLEX_SPC integrator = md emtol = 100.0 emstep = 0.005 dt = 0.002 ; ps ! nsteps = 2500 ; total 50 ns nstcomm = 5000 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 12 rcoulomb = 12 rvdw = 12 coulombtype = PME fourierspacing = 2 pme_order = 6 optimize_fft = yes Tcoupl = v-rescale tc-grps = Protein Non-Protein ;tau_t = 0.1 0.1 tau_t = 0.2 0.2 ref_t = 300 300 energygrps = A-chain B-chain SOL NA Pcoupl = berendsen Pcoupltype = isotropic ;tau_p = 0.1 tau_p = 0.25 compressibility = 5.4e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] increasing cut-off and PME grid spacing
If the simulation is even stable, it will be horribly inaccurate. 12 nm cutoffs are unheard of and 2-nm grid spacing is about 20 times too large. Without seeing the original .mdp file that gave the high PME load, and without a further description about how large the system is (number of atoms), it is hard to say what you should do. Some system do not parallelize well, but I imagine you should be able to get better performance. -Justin Thank you for reply The original .mdp is below and the number of atoms is 20171 The difference is only in rlist, rcoulomb, rvdw, and fourierspacing title = ttt cpp = /lib/cpp constraints = hbonds ;define = -DFLEX_SPC integrator = md emtol = 100.0 emstep = 0.005 dt = 0.002 ; ps ! nsteps = 2500 ; total 50 ns nstcomm = 5000 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1 rcoulomb = 1 rvdw = 1 coulombtype = PME fourierspacing = 0.2 pme_order = 6 optimize_fft = yes Tcoupl = v-rescale tc-grps = Protein Non-Protein ;tau_t = 0.1 0.1 tau_t = 0.2 0.2 ref_t = 300 300 energygrps = A-chain B-chain SOL NA Pcoupl = berendsen Pcoupltype = isotropic ;tau_p = 0.1 tau_p = 0.25 compressibility = 5.4e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] increasing cut-off and PME grid spacing
Hi, Justin Sorry for the unclear message. My box vector in .gro file are 44.22834#160; 44.22834#160; 44.22834 and the number of atoms is 20171 The output of grompp is shown below, I don't know if it is enough and I'm sorry I don't know how should I do after you reply. Could you please give me more messages in detail? Hsin-Lin --- #160;#160;#160;#160;#160;#160;#160; Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, #160;#160;#160;#160;#160; Aldert van Buuren, P#228;r Bjelkmar, Rudi van Drunen, Anton Feenstra, #160;#160;#160;#160;#160;#160;#160; Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, #160;#160;#160;#160;#160;#160;#160;#160;#160;#160; Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; Michael Shirts, Alfons Sijbers, Peter Tieleman, #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; Berk Hess, David van der Spoel, and Erik Lindahl. #160;#160;#160;#160;#160;#160; Copyright (c) 1991-2000, University of Groningen, The Netherlands. #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; Copyright (c) 2001-2010, The GROMACS development team at #160;#160;#160;#160;#160;#160;#160; Uppsala University The Royal Institute of Technology, Sweden. #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; check out http://www.gromacs.org for more information. #160;#160;#160;#160;#160;#160;#160;#160; This program is free software; you can redistribute it and/or #160;#160;#160;#160;#160;#160;#160;#160;#160; modify it under the terms of the GNU General Public License #160;#160;#160;#160;#160;#160;#160;#160; as published by the Free Software Foundation; either version 2 #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; of the License, or (at your option) any later version. #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; :-)#160; grompp#160; (-: Option#160;#160;#160;#160; Filename#160; Type#160;#160;#160;#160;#160;#160;#160;#160; Description #160; -f#160;#160;#160;#160;#160;#160; test.mdp#160; Input#160;#160;#160;#160;#160;#160;#160; grompp input file with MD parameters #160;-po#160;#160;#160;#160;#160; mdout.mdp#160; Output#160;#160;#160;#160;#160;#160; grompp input file with MD parameters #160; -c#160; ../3eq/eq.gro#160; Input#160;#160;#160;#160;#160;#160;#160; Structure file: gro g96 pdb tpr etc. #160; -r#160;#160;#160;#160;#160;#160; conf.gro#160; Input, Opt.#160; Structure file: gro g96 pdb tpr etc. #160;-rb#160;#160;#160;#160;#160;#160; conf.gro#160; Input, Opt.#160; Structure file: gro g96 pdb tpr etc. #160; -n ../initial/index.ndx#160; Input, Opt!#160; Index file #160; -p ../initial/insulin.top#160; Input#160;#160;#160;#160;#160;#160;#160; Topology file #160;-pp#160; processed.top#160; Output, Opt. Topology file #160; -o#160;#160;#160;#160;#160;#160; test.tpr#160; Output#160;#160;#160;#160;#160;#160; Run input file: tpr tpb tpa #160; -t#160; ../3eq/eq.trr#160; Input, Opt!#160; Full precision trajectory: trr trj cpt #160; -e#160;#160;#160;#160;#160;#160; ener.edr#160; Input, Opt.#160; Energy file Option#160;#160;#160;#160;#160;#160; Type#160;#160; Value#160;#160; Description -- -[no]h#160;#160;#160;#160;#160;#160; bool#160;#160; no#160;#160;#160;#160;#160; Print help info and quit -[no]version bool#160;#160; no#160;#160;#160;#160;#160; Print version info and quit -nice#160;#160;#160;#160;#160;#160;#160; int#160;#160;#160; 0#160;#160;#160;#160;#160;#160; Set the nicelevel -[no]v#160;#160;#160;#160;#160;#160; bool#160;#160; no#160;#160;#160;#160;#160; Be loud and noisy -time#160;#160;#160;#160;#160;#160;#160; real#160;#160; -1#160;#160;#160;#160;#160; Take frame at or first after this time. -[no]rmvsbds bool#160;#160; yes#160;#160;#160;#160; Remove constant bonded interactions with virtual #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; sites -maxwarn#160;#160;#160;#160; int#160;#160;#160; 0#160;#160;#160;#160;#160;#160; Number of allowed warnings during input #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; processing. Not for normal use and may generate #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; unstable systems -[no]zero#160;#160;#160; bool#160;#160; no#160;#160;#160;#160;#160; Set parameters for bonded interactions without #160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; defaults to zero instead
[gmx-users] reference structure of g_rms
Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result. Could someone tell me what cause the different and which choice is better? And my version is gromacs v4.0.5 Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] reference structure of g_rms
Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result. I think they should give the same result. If not, then the mostly likely explanation is that you've not used the files the way you think you have. You need to be able to issue grompp -f md -c pr -o md g_rms -s md.tpr -f whatever g_rms -s pr.gro -f whatever and get different results for there to be some kind of problem. In any case, you need to provide copies of your command lines and the different result in order for us to see whether you or GROMACS has done something wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do something else with our time :-) Mark Hi, I checked the result again The order of the different is less than 0.1 nm. So that means this different is caused by precision? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] reference structure of g_rms
Hi Tsjerk, It's very helpful information. Thank you very much Sincerely yours, Hsin-Lin Hi Hsin-Lin, If you use a .tpr file, you perform a mass-weighted fit and analysis. A .gro file has no masses and thus the fit and analysis are performed non-mass weighted, which will give differences, depending on the selection for the analysis. Hope it helps, Tsjerk 2011/8/17 Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw: Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result. I think they should give the same result. If not, then the mostly likely explanation is that you've not used the files the way you think you have. You need to be able to issue grompp -f md -c pr -o md g_rms -s md.tpr -f whatever g_rms -s pr.gro -f whatever and get different results for there to be some kind of problem. In any case, you need to provide copies of your command lines and the different result in order for us to see whether you or GROMACS has done something wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do something else with our time :-) Mark Hi, I checked the result again The order of the different is less than 0.1 nm. So that means this different is caused by precision? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] disulfide bond, molecule type
/ // I doubt the chain identifiers are relevant. Both .gro and .pdb files should // display properly. The only odd instance I can think of is that without separate // chains, some programs may interpret the protein coordinates as a single // molecule, but I would think that would only happen in the rarest of cases (when // the termini are so close that the heuristic bond search algorithms think there // should be a bond between the chains). // // When invoking trjconv, did you use any option to modify the periodic representation? // I used // trjconv -pbc mol -center -n index.ndx .. / OK, so this was just a periodicity issue all along. I'm sorry that I don't understand. So I did something wrong in PBC by trjconv? And I tried another way. I change the content of .gro file. I plus the number of residues in A-chain to B-chain's residue number. And this new gro file shows the correct snapshot in VMD. for example my a-chain has 21 residues, b-chain has 30 residues. In output .gro file the residue number is 1 to 21 and 1 to 30. I'm afraid VMD got confused for the repeat number 1 to 21. So I change 1-30 in b-chain to 22-51. Then snapshot in VMD become correct. / Here I chose a-chain for center and protein for output. // / Do I have any commend can use instead of chain identifier A and B // // mannually? // // // / // I don't understand your question here. // I'm sorry. // I separate chains manually. // (Add chain identifier A and B manually in vim) // Do I have any commend of GROMACS can handle this and I don't need to // separate chains manually. // / With a merged chain, I think you will always have to add them back in. Thank you. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] disulfide bond, molecule type
No. You said before you had broken chains. Applying trjconv -pbc mol fixes this issue. Molecules can be broken across periodic boundaries and is an entirely normal phenomenon. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions / And I tried another way. // I change the content of .gro file. // I plus the number of residues in A-chain to B-chain's residue number. // And this new gro file shows the correct snapshot in VMD. // for example // my a-chain has 21 residues, b-chain has 30 residues. // In output .gro file the residue number is 1 to 21 and 1 to 30. // // I'm afraid VMD got confused for the repeat number 1 to 21. // So I change 1-30 in b-chain to 22-51. // Then snapshot in VMD become correct. / Then this was primarily VMD's issue. -Justin Thank you for your help. I think I have no problem now. Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] disulfide bond, molecule type
Hi, I'm trying to heat a protein. There are two chains, A-chain and B-chain. Two disulfide bonds are between A-chain and B-chain. As I know, I should let A-chain and B-chain belong to the same [molecule type] in .top file if I want to have the two inter-bonds. So, I delete the TER line between A-chain and B-chain in .pdb file. And then I use pdb2gmx -chainsep interactive on it . I got the two bonds successfully. But after heating, the length of A-chain and B-chain in VMD was changed. The number of residues in A-chain increase and the ones of B-chain decrease. It means some residues move from B-chain to A-chain. How should I prevent this kind of error happen. Besides, I found even though I only have protein_A which consist both of A-chain and B-chain. The number of first residue of B-chain is started from 1 in .gro file. I thought it should be equal to the number of A-chain's residues plus 1. And it was also strange that the number of first water molecules was equal to the number of B-chain plus 1 I thought it should be equal to the number of A-chain's residues plus the number of B-chain's residues plus 1 Is it a bug? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] disulfide bond, molecule type
Hsin-Lin Chiang wrote: / Hi, // // I'm trying to heat a protein. // There are two chains, A-chain and B-chain. // Two disulfide bonds are between A-chain and B-chain. // As I know, I should let A-chain and B-chain belong to the same [molecule // type] in .top file if I want to have the two inter-bonds. // // So, I delete the TER line between A-chain and B-chain in .pdb file. // And then I use pdb2gmx -chainsep interactive on it . // // I got the two bonds successfully. // But after heating, the length of A-chain and B-chain in VMD was changed. // The number of residues in A-chain increase and the ones of B-chain // decrease. // It means some residues move from B-chain to A-chain. // How should I prevent this kind of error happen. // / The labeling changes? Is this something VMD is doing or something you can actually demonstrate in the coordinate file? Labeling didn't change. I don't know what VMD did. It seems to some residues disappear, A-chain was elongated, and B-chain was shortened. I also tried Pymol. It gave me several small crash peptides. But I just tried Ramol, everything looks correct. Something wrong in VMD and Pymol may just because A-chain and B-chain curved extremely after heating. But I'm still afraid Is my output structure wrong by GROMACS? Sincerely yours, Hsin-Lin / Besides, I found even though I only have protein_A which consist both of // A-chain and B-chain. // The number of first residue of B-chain is started from 1 in .gro file. // I thought it should be equal to the number of A-chain's residues plus 1. // // And it was also strange that the number of first water molecules was // equal to the number of B-chain plus 1 // I thought it should be equal to the number of A-chain's residues plus // the number of B-chain's residues plus 1 // // Is it a bug? // / No, it is the expected output. By default, pdb2gmx does not renumber residues consecutively. This feature was introduced some time ago so that output selections could easily be made in multiple chain molecules like this one. If you want residues renumbered consecutively, either post-process the coordinate files with genconf -renumber or start over and use pdb2gmx -renum. Thank you for your explanation. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] disulfide bond, molecule type
If you have heated your system severely, you may have generated an unstable system that is on the verge of crashing. VMD seems to allude to some weird geometry and PyMOL would seem to confirm that. I don't know why Rasmol appears OK. If you've somehow lost residues then they probably have infinite coordinates and your simulation has blown up and is therefore junk. -Justin I convert .gro to .pdb by trjconv and add chain identifier A and B to .pdb file. (Because of -chainsep all chain identifier was delete before MD) Then VMD and Pymol shows correct as Rasmol. So, maybe the error of snapshot was just because chain identifiers were lacked before. Do I have any commend can use instead of chain identifier A and B mannually? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] disulfide bond, molecule type
I doubt the chain identifiers are relevant. Both .gro and .pdb files should display properly. The only odd instance I can think of is that without separate chains, some programs may interpret the protein coordinates as a single molecule, but I would think that would only happen in the rarest of cases (when the termini are so close that the heuristic bond search algorithms think there should be a bond between the chains). When invoking trjconv, did you use any option to modify the periodic representation? I used trjconv -pbc mol -center -n index.ndx .. Here I chose a-chain for center and protein for output. / Do I have any commend can use instead of chain identifier A and B // mannually? // / I don't understand your question here. I'm sorry. I separate chains manually. (Add chain identifier A and B manually in vim) Do I have any commend of GROMACS can handle this and I don't need to separate chains manually. Hsin-Lin -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About -chainsep and -ter
於 2011/7/21 上午 03:19, gmx-users-requ...@gromacs.org 提到: Hi everyone, My pdb file is consist of two chains with one intra- two inter-disulfide bonds. So I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter (I have deleted the TER and OXT lines of A-chain.) I'm not sure if I need to use -ter here, I don't understand the meaning of interective termini selection, iso charged . The -ter option allows you to change the protonation state of the termini. The shorthand iso means instead of, implying that charged termini are the default. If you do not need to alter the protonation state of the termini, then you do not need the -ter option. Thanks for the explain. Anyway, I met problem after editconf, genbox, grompp, genion, and grompp. When I execute mdrun, I got the warning and terminated. Please see the long message below my name. Your system exploded because pdb2gmx likely tried to make your two chains one continuous protein, forming an unrealistic bond between the C-terminal of chain A and the N-terminal of chain B. By removing the TER delimiter, you've essentially told pdb2gmx that you have one protein, not two. If I don't use -chainsep ter, then pdb2gmx will consider two chains as Protein-A and Protein-B. The inter-disulfide bonds between two-chains will be lost. However, if I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep interactive and selected y. Then everything is OK in mdrun step. I don't know what the different in -chainsep interactive and -chainsep ter is in my case. Assuming that the y response indicates that you want separate chains, that's why this approach works. Regardless, if you have two distinct proteins (i.e. the backbones are not continuous), you do not want the chains to be considered continuous. Disulfides are created in a separate mechanism utilizing specbond.dat and is independent of the use of -chainsep. The question is , Merge chain ending with residue ASN21 (chain id 'A', atom 163OXT) with chain starting with residue PHE1 (chain id 'B', atom 165 N)? [n/y] Then I choose y, I think it's the same as -chainsep ter. Isn' it? But for -chainsep ter, there is errors in mdrun. For -chainsep interactive and type y, everything correct. They seems to the same in my two chain system. There is likely some difference (probably a single bond) that is causing the problem. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About -chainsep and -ter
Please post a diff of the two topologies (the one that failed and the one that worked). -Justin I use diff bash commend on the two top file and save to log file. The different was long but they both have three inter-disulfide bond There are 3973 lines in different log file.#160; I'm not sure if I can post all here. Do we have another way to discuss? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About -chainsep and -ter
I suspect this is a bug, so I have filed an issue on redmine: http://redmine.gromacs.org/issues/784 In a previous issue (http://redmine.gromacs.org/issues/544), the -chainsep interactive option did not work, but now it does. Conversely, -chainsep ter (which should also work in this case) does not. -Justin I get success in pdb2gmx, but I not only delete ter line but also all OXT lines according to this mailing list, http://www.mail-archive.com/gmx-users@gromacs.org/msg33251.html But I'm failed when I used mdrun in -chainsep ter case. Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About -chainsep and -ter
Right. Even if you somehow force pdb2gmx to write a topology in this case, the bonds are not correct and the termini are incomplete. That will hopefully be resolved when the bug is fixed. For now, you have a workaround. Just use -chainsep interactive and you will get a proper topology. -Justin I understand now. Thank you very much for your help. Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About -chainsep and -ter
Hi everyone, My pdb file is consist of#160; two chains with one intra- two inter-disulfide bonds. So I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter (I have deleted the TER and OXT lines of A-chain.) I'm not sure if I need to use -ter here, I don't understand the meaning of interective termini selection, iso charged . Anyway, I met problem after editconf, genbox, grompp, genion, and grompp. When I execute mdrun, I got the warning and terminated. Please see the long message below my name. However, if I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep interactive#160; and selected y. Then everything is OK in mdrun step. I don't know what the different in -chainsep interactive and -chainsep ter is in my case. They seems to the same in my two chain system. Sincerely yours, Hsin-Lin - starting mdrun 'Protein in water' 750 steps,#160; 15000.0 ps. Warning: 1-4 interaction between 196 and 207 at distance 3.231 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step 0, time 0 (ps)#160; LINCS WARNING relative constraint deviation after LINCS: rms 66.078426, max 708.612183 (between atoms 207 and 208) bonds that rotated more than 30 degrees: #160;atom 1 atom 2#160; angle#160; previous, current, constraint length #160;#160;#160; 207#160;#160;#160; 208#160;#160; 90.0#160;#160;#160; 0.1000#160; 70.9612#160;#160;#160;#160;#160; 0.1000 Back Off! I just backed up step0b.pdb to ./#step0b.pdb.4# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4# Wrote pdb files with previous and current coordinates Step 1, time 0.002 (ps)#160; LINCS WARNING relative constraint deviation after LINCS: rms 67071649.681650, max 719263296.00 (between atoms 207 and 208) bonds that rotated more than 30 degrees: #160;atom 1 atom 2#160; angle#160; previous, current, constraint length #160;#160;#160; 207#160;#160;#160; 208#160;#160; 90.0#160;#160; 70.9612 71926328.#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 212#160;#160;#160; 213#160;#160; 90.0#160;#160;#160; 0.1090#160;#160; 0.1308#160;#160;#160;#160;#160; 0.1090 #160;#160;#160; 216#160;#160;#160; 217#160;#160; 40.3#160;#160;#160; 0.1090#160;#160; 0.1090#160;#160;#160;#160;#160; 0.1090 #160;#160;#160; 218#160;#160;#160; 219#160;#160; 90.0#160;#160;#160; 0.1090#160;#160; 0.1545#160;#160;#160;#160;#160; 0.1090 #160;#160;#160; 224#160;#160;#160; 225#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.3996#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 232#160;#160;#160; 233#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.3867#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 238#160;#160;#160; 239#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.1782#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 238#160;#160;#160; 240#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 1.0652#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 243#160;#160;#160; 244#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.3092#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 250#160;#160;#160; 251#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.3082#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 250#160;#160;#160; 252#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.2102#160;#160;#160;#160;#160; 0.1000 step 1: Water molecule starting at atom 10744 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1b.pdb to ./#step1b.pdb.4# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.4# Wrote pdb files with previous and current coordinates Segmentation fault #160; -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Can't unfold the protein
Hi, I have question about unfolding. I use three different ways respectively but all failed. The three way is, 1. 600K in 20ns, then the system explode. 2. 400K in 10ns, the protein is very stable and the value is almost the same in radius of gyration. 3. heating up from 300K to 400K in 2ns and the other 2ns for 400K only, then the protein is still stable and the value is almost the same in radius of gyration. Below is the mdp file of the heating. What's wrong with my system? regards, Hsin-Lin - title#160;#160;#160;#160;#160;#160;#160; = ttt cpp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; /lib/cpp constraints#160;#160;#160;#160;#160;#160;#160;#160; =#160; hbonds ;define#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; -DFLEX_SPC integrator#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; md emtol#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 100.0 emstep#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.005 dt#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.002#160;#160;#160; ; ps ! nsteps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 200#160; ; total 4 ns nstcomm#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstxout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstvout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstfout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstlog#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstenergy#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 500 nstlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 5 ns_type#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; grid rlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 1. rcoulomb#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 1. rvdw#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 1. coulombtype#160;#160;#160;#160;#160;#160;#160;#160; =#160; PME fourierspacing#160;#160;#160;#160;#160; =#160; 0.12 pme_order#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 4 optimize_fft#160;#160;#160;#160;#160;#160;#160; =#160; yes Tcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; v-rescale tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; Protein Non-Protein ;tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.1#160; 0.1 tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.2 0.2 ref_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 300 300 energygrps#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; A-chain B-chain SOL#160; NA+ Pcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; berendsen Pcoupltype#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; isotropic ;tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.1 tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 0.25 compressibility#160;#160;#160;#160; =#160; 5.4e-5 ref_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 1.0 gen_vel#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; yes gen_temp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 300 gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 173529 ; Annealing annealing#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; single single annealing_npoints#160;#160; =#160; 21 21 annealing_time#160;#160;#160;#160;#160; =#160; 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 annealing_temp#160;#160;#160;#160;#160; =#160; 300 305 310 315 320 325 330 335 340 345 350 355 360 365 370 375 380 385 390 395 400 300 305 310 315 320 325 330 335 340 345 350 355 360 365 370 375 380 385 390 395 400 - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Can't unfold the protein
Dear Chris, Thank you for your reply. My protein is very stable. I simulated it in 300ns in 300K before but there was almost no change. That's why I want to do denaturation now. I want to start a new simulation on the protein which is unfolded. And I'll read the paper you told me. Thank you. But I don't understand what you recommend me to do. You use 3000K on your protein and the protein unfolded. I use 600K on my protein but the system explode(box become very big and protein locate at corner). I saw the second way on this web, http://manual.gromacs.org/online/protunf.html But it also useless to me. And in my mdp I use thermostat and barostat, which means my system is NPT. Does anything wrong in my methods? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun -nc
Hi, I tried gromacs 4.5.4 in these days and last version I used is 4.0.5. I found when I add --enable-threads in installation. I can use mdrun -nc 12 to run 12 CPUs together within one machine. It also amazing me when I type top to check the job, only one process in computer and the CPU utility is 1200%!! But I tried to execute it on two machines, then the second machines didn't work. I don't need mdrun_mpi any more because mdrun -nc is faster the mdrun_mpi. That make me confused. Am I right to use mdrun -nc to run parallel job in this way? Does the result is the same as which is employed by mdrun_mpi? (Exactly I never use mdrun_mpi more than one machine since the ethernet between machines is very slow here.) If mdrun -nc is available. Do we have another commend support CPUs more than one in the same machine. Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Re: Error of installing gromacs v4.5.4
Hi, Thank you. I use gcc v4.4 and complete the installing. Sincerely yours, Hsin-Lin Hi, That compiler is ancient (thought it might have SSE2 support) as well as the OS, I guess (RHEL 3?). Still, the CPU does support SSE2 so if you can get a gcc 4.1 or later on it you should still be able compile and run the code without a problem. -- Szil獺rd 2011/5/26 Hsin-Lin Chiang jian...@phys.sinica.edu.tw: Hi, Thank you for your reply. I'm not so good in computer. I think the platform you ask me is Linux, and kernel is 2.4.21-60.ELsmp The compiler is gcc v3.2.3 in the machine in my institute. Sincerely yours, Hsin-Lin Message: 1 Date: Thu, 26 May 2011 18:03:09 +0200 From: Szil?rd P?ll szilard.p...@cbr.su.se Subject: Re: [gmx-users] Error of installing gromacs v4.5.4 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTi=9v3+1dnbjsmd6hna-ayfdprb...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Hsin-Lin, Your problem are caused by a missing header file which is included by the nobonded SSE kernels which is indicated by the first error in your output: nb_kernel400_ia32_sse.c:22:23: emmintrin.h: No such file or directory This header is needed for SSE and SSE2, but for some reason you don't have it. What platform are you compiling on/for and what compiler are you using? Alternatively, you can turn off acceleration and you'll be able to compile the code, but it will run *much* slower than with the accelerated kernels. -- Szil憳削 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Error of installing gromacs v4.5.4
Hi, Thank you for your reply. I'm not so good in computer. I think the platform you ask me is Linux, and kernel is 2.4.21-60.ELsmp The compiler is gcc v3.2.3 in the machine in my institute. Sincerely yours, Hsin-Lin Message: 1 Date: Thu, 26 May 2011 18:03:09 +0200 From: Szil?rd P?ll szilard.p...@cbr.su.se Subject: Re: [gmx-users] Error of installing gromacs v4.5.4 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTi=9v3+1dnbjsmd6hna-ayfdprb...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Hsin-Lin, Your problem are caused by a missing header file which is included by the nobonded SSE kernels which is indicated by the first error in your output: nb_kernel400_ia32_sse.c:22:23: emmintrin.h: No such file or directory This header is needed for SSE and SSE2, but for some reason you don't have it. What platform are you compiling on/for and what compiler are you using? Alternatively, you can turn off acceleration and you'll be able to compile the code, but it will run *much* slower than with the accelerated kernels. -- Szil嫫d -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] different output generated by continue and discontinue simulation
be the same, right? Is anything wrong in my work? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] different output generated by continue and discontinue simulation
method generate a stable movie and fluctuation of interaction energy. Theotically these two should be the same, right? Is anything wrong in my work? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] different output generated by continue and discontinue simulation
Sorry for the abnormal code.
I have fixed that.
---
Hi,
My gromacs version is 4.0.5.
I used grompp to generate tpr for 1ps simulation in this way
grompp -f md1.mdp -n index.ndx#160; -p topol.top -c 0ps.gro#160; -t 0ps.trr
-o 1ps.tpr
mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro
Here is my md1.mdp file:
;
title = ttt
cpp = /lib/cpp #160;
constraints = hbons
;define = -DFLEX_SPC #160;
integrator = md#160;
emtol = 100.0
emstep = 0.005#160;
dt = 0.002 ; ps!
nsteps = 500 ; total 1ps
nstcomm = 500 #160;
ntsxout = 500 #160;
ntsvout = 500#160;
ntsfout = 500 #160;
ntslog = 500#160;
nstenergy = 500
nstlist = 5#160; #160;
ns_type = grid #160;
rlist = 1.
rcoulomb = 1.
rvdw = 1.
coulombtype = PME
fourierspacing = 0.12
pme_order = 4
optimize_fft = yes
Tcoupl = v-rescale
rc-grps = A-chain B-chain drug SOL NA+
;tau_t = 0.1 0.1
tau_t =0.2 0.2 0.2 0.2
ref_t = 300.00 300.00 300.00 300.0 300.00
energygrps = A-chain B-chain druhg SOL NA+
Pcoupl = berendsen
Pcoupltype = isotropic
;tau_p = 0.1
tau_p = 0.25
compressibility = 5.4e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300.00
gen_seed = 173531
gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; 173531
--
Then I execute below loop in other 5 times for the totaly 60ns
trajectories.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -t
${n-1}ps.trr -o ${n}ps.tpr
mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro
The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no.
Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory to
continue.(I didn't really use this commend $(n-1) in bash script, it won't
work.)
I change the other way to run parallel simulation on the same system fordouble
check since above script is difficult to parallelize in public computer.
The new method is:
grompp -f md60ns.mdp -n index.ndx#160; -p topol.top -c 0ps.gro#160; -t
0ps.trr -o 60ns.tpr
mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c
60ns.gro
The only different between md1.mdp and md60ns.mdp is nstep=3000 in
md60ns.mdp.
Theses two data generated by different ways are totaly different.
Here I mean different is not on the number buy mean the tendency of figure.
In the movie of first method, protein runs violently and go outside the
periodic boundary and then split by cubic edge.
The interaction energy within protein also fluctuate in an unstable way.
On the contrary, the second method generate a stable movie and fluctuation of
interaction energy.
Theotically these two should be the same, right?
Is anything wrong in my work?
Sincerely yours,
Hsin-Lin
--- End of Forwarded Message ---
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[gmx-users] different output generated by continue and discontinue simulation
Hi, Mark
tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
=#160; A-chain B-chain drug SOL#160; NA+
This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats
Thank you for your website.#160; I understand now.
grompp -f md2.mdp -n index.ndx#160; -p topol.top -c ${n-1}ps.gro#160; -t
${n-1}ps.trr -o ${n}ps.tpr
mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro
You are following neither of the approaches recommended here
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
Ya, I'm sorry but my colleborator give me that before.
It is similiar to the commends connect position restrained dynamics and MD.
You can find grompp read gro and trr of last time frame to make a tpr file of
next time frame.
I thought this cause the time write on each snapshot is 0, but the dynamics is
still processing.
Did I miss something?
You say the pressure-coupling will be lost in each ps, does it mean that trr
file doesn't have this message inside?
Theses two data generated by different ways are totaly different.
Here I mean different is not on the number buy mean the tendency of figure.
See http://www.gromacs.org/Documentation/Terminology/Reproducibility
Ya, I know this since last time you show me this web in mailing list.
Thank you again.
But the different between these two outputs is totaly different.
I have four systems with different parameter gen_seed.
First is always unstable and irregular, but second is stable and regular.
On the contrary, the second method generate a stable movie and fluctuation
of interaction energy.
Theotically these two should be the same, right?
The second is probably happier about not losing the pressure-coupling
information every 1ns. However only much
much longer trajectories should show mutual convergence, and the movie is not
a reasonable way to look for it.
Mark
Sorry I don't understand you here.
Do you mean second way seems to more correct?
And what kind of mutual convergence you mean here?
Does It mean I can try to find mutual convergence in output of second way?
I'm sorry for my stupid and poor English.
Sincerely yours,
Hsin-Lin
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[gmx-users] Inaccurate time frame
Hi, Mark, I'll adopt your suggestion. Thank you for your reply again. Sincerely yours, Hsin-Lin On 7/12/2010 6:01 PM, Hsin-Lin Chiang wrote: / // Ah, sorry, I didn't read you well enough. // // I've just seen that GROMACS 4.5 introduced trjconv -round to address // this kind of issue. I suppose you will find trjconv -round -split // works for you. // // Mark // Hi, Mark // // Thank you for your suggestion. // I'm sorry that my version is 4.0.5 // I think I can use -sep and write a shell script to combine frames // together. / That, or make a local installation of 4.5.3 and just use trjconv from it. There's no issue with trajectory compatibility of which I am aware. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Inaccurate time frame
Hi, My time unit is 1ps and today I have 300ns data generated by parallel simulation. I use trjconv -split 1000 on my trajectory but get the truncated end at t= 5000.0 Theoretically it should stop at t= 1000.000 I found that I don't have t= 1000.0 frame but have t= 1000.6, 2000.00012, 3000.00024, and t= 4000.00024. I know I can add -timestep 1 to solve this problem and let file can be truncated at t= 1000.6. How does this kind of inaccurate time frames happen? Is this trajectory a wrong result? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Inaccurate time frame
Hi, Mark Thank you for your reply. I know -skip -sep is more robust. Since the definition talked about nr-th frame but not nr-th ps. -skip int 1 Only write every nr-th frame -[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb file The problem is that -skip 1000 -sep didn't consist of several time frames in the same file but just write nr-th frame. That's why I use -split 1000 -timestep 1 according these definitions found in manual. -split time 0 Start writing new file when t MOD split = first time (ps) -timestep time 0 Change time step between input frames (ps) With -dt it is possible to reduce the number of frames in the output. This option relies on the accuracy of the times in your input trajectory, so if these are inaccurate use the -timestep option to modify the time (this can be done simultaneously). Would you please teach how to use -skip -sep to get the same kind of file which include all of 1000ps time frames together in a 1ns gro file? I'll appreciate to any helps. Sincerely yours, Hsin-Lin /Hi, // // My time unit is 1ps and today I have 300ns data generated by parallel simulation. // I use trjconv -split 1000 on my trajectory but get the truncated end at t= 5000.0 // Theoretically it should stop at t= 1000.000 // I found that I don't have t= 1000.0 frame but have t= 1000.6, 2000.00012, 3000.00024, and t= 4000.00024. // // I know I can add -timestep 1 to solve this problem and let file can be truncated at t= 1000.6. // // How does this kind of inaccurate time frames happen? // Is this trajectory a wrong result? // /I just wrote a FAQ+wiki page for this, since it gets asked a bit. Seehttp://www.gromacs.org/Documentation/Floating_Point_Arithmetic trjconv -skip -sep is a more robust approach here Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Inaccurate time frame
Ah, sorry, I didn't read you well enough. I've just seen that GROMACS 4.5 introduced trjconv -round to address this kind of issue. I suppose you will find trjconv -round -split works for you. Mark Hi, Mark Thank you for your suggestion. I'm sorry that my version is 4.0.5 I think I can use -sep and write a shell script to combine frames together. Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] extending simulation without cpt file
Hi, Today I use serach and find this topic. I got confused. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations According the page of extending simulation, in GROMACS ver.4, the commend is: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt I use this two lines to continue my simulation and get success. But now I'm much worried my data is wrong since I didn't use -e edr and -t trr as in the first line above. The way that tpbconv should -e -t files is written in the part ver. 3.3.3 and before. My GROMACS version is 4.0.5. Am I right to use lines above to do extending simulation? Hsin-Lin - Original Message - From: Yongchul Chung yxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS users gmx-users@gromacs.org Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint. Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr. Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I used it, I'd forgotten :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] extending simulation without cpt file
Hi, Mark So, You mean I can get correct extending simulation without using -e ede and -t trr in GROMACS ver.4. Then I can set my mind at rest. Thank you for your reply. Hsin-Lin Hi, Today I use serach and find this topic. I got confused. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations According the page of extending simulation, in GROMACS ver.4, the commend is: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr So you've created a new .tpr with a longer simulation time (but which incidentally has the state of the previous .tpr)... mdrun -s next.tpr -cpi previous.cpt ... and told mdrun to use that longer time, and the current state in the checkpoint file. This will work, so long as you are not attempting to change the thermodynamic ensemble, or similar. Mark I use this two lines to continue my simulation and get success. But now I'm much worried my data is wrong since I didn't use -e edr and -t trr as in the first line above. The way that tpbconv should -e -t files is written in the part ver. 3.3.3 and before. My GROMACS version is 4.0.5. Am I right to use lines above to do extending simulation? Hsin-Lin - Original Message - From: Yongchul Chungyxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS usersgmx-users@gromacs.org Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint. Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr. Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I used it, I'd forgotten :-) Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101122/437e2152/attachment.html -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_ hbond on two peptides
Hi, I use g_hbond to analyze the system with two peptide. And I introduce the ndx file which include two group for the two peptides respectively. For the first prompt of g_hbond, I choose the group of the first peptide. For the second prompt, I choose the other peptide. I got the data that announced 4 H-bonds were found. And then I use rasmol to check, I found there are 2 intra-H-bonds in first peptide and 2 intra-H-bonds in the second. There are no inter-H-bonds between two peptides in my system. It's strange since I had selected different group to analyze when g_hbond promted. How should I do to exclude the intra-H-bond on one peptide? Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: g_ hbond on two peptides
Hi, Erik and XAvier Thank you for your help I have had a idea to check my data. I selected the protein group two times and I get 5 H-bonds. Then I select first and second peptide group two time and get 0 and 1 H-bond respectively. And 5 minus 1 is equal to 4 that is equal to the number of H-bonds in my last message. So I think maybe it's just because the manners of two programs are different. regards, Hsin-Lin Hsin-Lin Chiang skrev: Hi, I use g_hbond to analyze the system with two peptide. And I introduce the ndx file which include two group for the two peptides respectively. For the first prompt of g_hbond, I choose the group of the first peptide. For the second prompt, I choose the other peptide. I got the data that announced 4 H-bonds were found. And then I use rasmol to check, I found there are 2 intra-H-bonds in first peptide and 2 intra-H-bonds in the second. There are no inter-H-bonds between two peptides in my system. It's strange since I had selected different group to analyze when g_hbond promted. How should I do to exclude the intra-H-bond on one peptide? Hsin-Lin That sounds strange indeed. Have you looked into which hbonds are found? And are you sure your index file is error free? You may also want to check that both programs define H-bond in the same manner. /Erik -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 73, Issue 177
Hi ,Mark: I had announced my system is a dimer with each peptides have 6 residues. I'm sorry if I didn't express it to be understood easily. Can you please tell me why 13 coils are reasonable if my systems is a dimer? regards, Hsin-Lin Hi, Justin: I post my coordinate with protein translated by trjconv By this gro file, I get 0 structure and 13 coils. Haven't you been saying for what seems like weeks now that you have 12 residues in your protein? If so... snip C 70 2.223 2.893 1.484 -0.0883 0.1244 -0.1837 6ASN O1 71 2.111 2.941 1.505 -0.2557 -0.4837 -0.1041 6ASN O2 72 2.313 2.953 1.419 - 0.5561 0.0660 0.4455 Here, there's quite clearly an internal COO and NH3... hence it seems that you have two 6-residue chains. That's important data to be aware of, and to communicate to people who might help... Our belief that you really had a 12-residue peptide excludes this kind of issue from trouble-shooting, which ends up wasting everyone's time. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: the output of do_dssp
Hi ,Mark: I had announced that my system is a dimer with each peptides have 6 residues in my first post. I'm sorry if I didn't express it to be understood easily. Can you please tell me why 13 coils are reasonable if my systems is a dimer? regards, Hsin-Lin Hi, Justin: I post my coordinate with protein translated by trjconv By this gro file, I get 0 structure and 13 coils. Haven't you been saying for what seems like weeks now that you have 12 residues in your protein? If so... snip C 70 2.223 2.893 1.484 -0.0883 0.1244 -0.1837 6ASN O1 71 2.111 2.941 1.505 -0.2557 -0.4837 -0.1041 6ASN O2 72 2.313 2.953 1.419 - 0.5561 0.0660 0.4455 Here, there's quite clearly an internal COO and NH3... hence it seems that you have two 6-residue chains. That's important data to be aware of, and to communicate to people who might help... Our belief that you really had a 12-residue peptide excludes this kind of issue from trouble-shooting, which ends up wasting everyone's time. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: the output of do_dssp
Hi, Justin: I post my coordinate with protein translated by trjconv By this gro file, I get 0 structure and 13 coils. regards, Hsin-Lin Generated by trjconv : Protein in water t= 0.0 144 1LEU N1 2.499 1.707 2.735 -0.1664 0.1749 0.5034 1LEU H12 2.496 1.753 2.824 -0.0517 -2.4571 1.9862 1LEU H23 2.456 1.619 2.755 0.1871 0.0557 0.7811 1LEU H34 2.591 1.691 2.698 -0.0836 0.9027 0.3938 1LEU CA5 2.419 1.772 2.633 -0.3054 -0.5208 0.2431 1LEU CB6 2.277 1.809 2.687 0.1445 -0.1872 -0.2452 1LEU CG7 2.202 1.686 2.731 -0.2024 0.3028 0.1044 1LEUCD18 2.063 1.737 2.778 0.2195 0.2407 0.1571 1LEUCD29 2.197 1.583 2.615 0.2120 -0.5339 0.1770 1LEU C 10 2.479 1.897 2.572 0.1063 -0.1920 0.0451 1LEU O 11 2.483 2.008 2.627 0.2017 -0.4490 0.0233 2TYR N 12 2.493 1.882 2.437 -0.1877 -0.3169 -0.5678 2TYR H 13 2.446 1.812 2.384 0.6045 -1.4218 0.1228 2TYR CA 14 2.568 1.987 2.363 -0.2499 0.5688 -0.4543 2TYR CB 15 2.589 1.933 2.224 0.6646 -0.2988 -0.3037 2TYR CG 16 2.641 2.031 2.122 0.0017 0.2452 -0.1870 2TYRCD1 17 2.772 2.065 2.121 -0.4594 -0.2211 -0.0739 2TYRHD1 18 2.841 2.029 2.196 -0.1936 2.1660 0.9115 2TYRCD2 19 2.561 2.096 2.031 0.6321 -0.0604 0.5143 2TYRHD2 20 2.454 2.077 2.025 0.6551 0.1338 -0.9454 2TYRCE1 21 2.827 2.158 2.032 -0.1241 0.2352 -0.6043 2TYRHE1 22 2.935 2.169 2.027 -0.0121 -0.2184 0.4867 2TYRCE2 23 2.607 2.183 1.935 -0.7318 -0.3641 0.2984 2TYRHE2 24 2.537 2.240 1.874 2.4629 1.6445 -1.8271 2TYR CZ 25 2.744 2.223 1.938 -0.9702 -0.5296 0.3816 2TYR OH 26 2.796 2.320 1.854 0.1652 0.2056 -0.1630 2TYR HH 27 2.714 2.370 1.829 -0.0067 -0.1509 -0.3161 2TYR C 28 2.492 2.121 2.359 -0.9847 -0.4718 -0.5034 2TYR O 29 2.369 2.129 2.344 0.1513 0.3775 -0.1130 3GLN N 30 2.564 2.228 2.385 -0.2495 0.1552 0.8649 3GLN H 31 2.647 2.221 2.441 -0.1774 -3.6419 0.5524 3GLN CA 32 2.519 2.362 2.357 0.6342 0.0752 -0.4227 3GLN CB 33 2.615 2.451 2.432 0.3037 -0.2198 0.6973 3GLN CG 34 2.569 2.596 2.453 -0.2200 0.0688 -0.5109 3GLN CD 35 2.556 2.690 2.327 0.9953 0.3411 -0.2090 3GLNOE1 36 2.640 2.694 2.240 -0.9468 -0.2495 -0.6126 3GLNNE2 37 2.449 2.761 2.321 -0.4839 0.0971 -0.2517 3GLN HE21 38 2.384 2.757 2.397 -0.8822 0.9806 -0.5342 3GLN HE22 39 2.443 2.818 2.239 1.3155 1.4839 0.4945 3GLN C 40 2.501 2.401 2.207 0.2212 -0.2300 0.2782 3GLN O 41 2.596 2.416 2.125 -0.3813 -0.0351 0.0925 4LEU N 42 2.377 2.427 2.177 -0.1825 0.0192 -0.2668 4LEU H 43 2.302 2.432 2.243 1.4715 -0.4825 1.7638 4LEU CA 44 2.342 2.451 2.033 0.2037 0.0368 -0.1113 4LEU CB 45 2.230 2.360 1.985 -0.4049 -0.4174 -0.1918 4LEU CG 46 2.193 2.374 1.838 0.7678 -0.3161 0.4261 4LEUCD1 47 2.243 2.255 1.755 0.7379 0.9397 0.6576 4LEUCD2 48 2.041 2.401 1.828 -0.2357 0.6221 -0.0518 4LEU C 49 2.300 2.600 2.014 0.1156 -0.7579 0.2678 4LEU O 50 2.183 2.641 2.032 0.0777 -0.1884 0.5428 5GLU N 51 2.402 2.676 1.977 0.1065 0.0801 -0.1886 5GLU H 52 2.499 2.669 2.001 -0.3871 0.9888 2.3980 5GLU CA 53 2.367 2.813 1.924 -0.4424 0.3677 0.0128 5GLU CB 54 2.465 2.914 1.989 -0.0708 -0.1784 0.3292 5GLU CG 55 2.431 3.059 2.017 0.0676 0.0058 -0.4907 5GLU CD 56 2.423 3.160 1.897 -0.1295 0.3354 0.1946 5GLUOE1 57 2.530 3.183 1.835 0.3233 -0.4874 0.7816 5GLUOE2 58 2.313 3.196 1.854 0.6508 -0.0618 0.6984 5GLU C 59 2.391 2.807 1.773 0.6638 -0.1591 -0.6210 5GLU O 60 2.500 2.836 1.726 -0.0179 -0.4997 -0.0116 6ASN N 61 2.278 2.810 1.704 -0.1838 -0.0571 0.1524 6ASN H 62 2.193 2.843 1.747 -1.7146 -1.5150 -1.5696 6ASN CA 63 2.278 2.779 1.562 -0.0805 -0.8216 0.6185 6ASN CB 64 2.200 2.652 1.531 -0.5886 -0.3894 -0.0808 6ASN CG 65 2.285 2.528 1.538 -0.1917 0.0598 0.1828 6ASNOD1 66 2.367 2.510 1.624 -0.1949 0.0958 0.2131 6ASNND2 67 2.262 2.432 1.453 -0.0713 0.3669 0.1154 6ASN HD21 68 2.176 2.451 1.407 -1.5107 -0.4210 2.3205 6ASN HD22 69 2.323 2.356 1.434 -0.8178 -0.7718 1.9579 6ASN C 70 2.223 2.893
[gmx-users] Re: the output of do_dssp
Hi, Justin: Thank you for your reply. I try to select the group, 'mainchain', when prompted, and get the quantity of coil still larger than the number of residues of my protein. The data is the same as the output that generated by the selection, 1. Protein. If I select backbone, I get the fatal error: Failed to execute command: /Prousr/statphys/hsinlin/dssp/dsspcmbi -na ddhIPvCe ddJ6Yv7a /dev/null 2 /dev/null And I don't understand even if I can run the selection, backbone, successfully. According the dssp web of wiki: http://en.wikipedia.org/wiki/DSSP_%28protein%29 the hydrogen bonds are dicided by O, C, H, and N four atoms. How can we get dssp analysis by backbone that includes only NCCNCCNCC.? Sincerely yours, Hsin-Lin Hsin-Lin wrote: Hi, I use do_dssp to generate xvg file collect the last line to make a plot. There are something written in this way: -- @ s0 legend Structure @ s1 legend Coil @ s2 legend Bend 0514 1 --- My system is dimer and each peptide has 6 residue. Then you have a problem. Your output indicates 14 residues are in a random coil, so either you have more than 12 total residues, or something went wrong in the dssp calculation. And the number I choose to analyze is 1. Protein. Perhaps this is why you had a problem. Normally, choosing Protein would cause the calculation to hang, but maybe that is not the case any more. See here for the proper group to choose and the rationale: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Now I have a question, if I want to calculate the percentage of secondary structure. In the example above, is it calculated in this way 5/12=42%? I'd question your results first...you don't have 12 residues in your calculation, otherwise your protein is 14/12 = 117% random coil! Also realize that (by default) the Structure term only includes alpha helix, beta strand, bend, and turn. Other structural elements are not included. That may or may not be what you want, depending on the structural elements of your protein. -Justin Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: the output of do_dssp
Hi, Justin Thank you for your patience. According your reply, I used trjconv to write only protein group into another file. I execute do_dssp again in group proteinand mainchain respectively but still get coils more than total residues. Why? Hsin-Lin Hsin-Lin wrote: Hi, Justin: Thank you for your reply. I try to select the group, 'mainchain', when prompted, and get the quantity of coil still larger than the number of residues of my protein. Then some other elements of your system are being detected as containing relevant atoms. What happens if you run do_dssp on a single structure containing only your protein? The data is the same as the output that generated by the selection, 1. Protein. If I select backbone, I get the fatal error: Failed to execute command: /Prousr/statphys/hsinlin/dssp/dsspcmbi -na ddhIPvCe ddJ6Yv7a /dev/null 2 /dev/null And I don't understand even if I can run the selection, backbone, successfully. No, you can't. According the dssp web of wiki: http://en.wikipedia.org/wiki/DSSP_%28protein%29 the hydrogen bonds are dicided by O, C, H, and N four atoms. How can we get dssp analysis by backbone that includes only NCCNCCNCC.? You can't - DSSP requires the presence of the carbonyl O in order to determine hydrogen bonding geometry. If you don't have a full carbonyl, the analysis fails. -Justin Sincerely yours, Hsin-Lin Hsin-Lin wrote: Hi, I use do_dssp to generate xvg file collect the last line to make a plot. There are something written in this way: -- @ s0 legend Structure @ s1 legend Coil @ s2 legend Bend 0514 1 --- My system is dimer and each peptide has 6 residue. Then you have a problem. Your output indicates 14 residues are in a random coil, so either you have more than 12 total residues, or something went wrong in the dssp calculation. And the number I choose to analyze is 1. Protein. Perhaps this is why you had a problem. Normally, choosing Protein would cause the calculation to hang, but maybe that is not the case any more. See here for the proper group to choose and the rationale: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Now I have a question, if I want to calculate the percentage of secondary structure. In the example above, is it calculated in this way 5/12=42%? I'd question your results first...you don't have 12 residues in your calculation, otherwise your protein is 14/12 = 117% random coil! Also realize that (by default) the Structure term only includes alpha helix, beta strand, bend, and turn. Other structural elements are not included. That may or may not be what you want, depending on the structural elements of your protein. -Justin Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the output of do_dssp
Hi, I use do_dssp to generate xvg file collect the last line to make a plot. There are something written in this way: -- @ s0 legend Structure @ s1 legend Coil @ s2 legend Bend 0514 1 --- My system is dimer and each peptide has 6 residue. And the number I choose to analyze is 1. Protein. Now I have a question, if I want to calculate the percentage of secondary structure. In the example above, is it calculated in this way 5/12=42%? Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parallel simulation in dual core PC
Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. How can I do for that? Any and all assistance is greatly appreciated. Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] output of dssp
Hi, I used do_dssp_d to analyze my data. The commend was written in this way: do_dssp_d -f a.gro -s a.tpr -n a.ndx -sc dssp.xvg There are three output, #ddXB2RJu.1#, ss.xpm and dssp.xvg, be generated. What is the first output file? It is generated automatically but with nothing inside. And in my analysis I only need xvg file. How can I do to get xvg output without the others accompanied? Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs, lam and condor
Hi,
I tried to use 4 and 8 CPUs.
There are about 6000 atoms in my system.
The interconnect of our computer is the network with speed 1Gb but not optical
fiber.
I'm sorry for my poor English and I couldn't express well in my question.
Everytime I submitted the parallel job, the nodes assigned to mehave been 100%
loading,
and the CPU source availble to me is less then 10%.
I think there is something wrong with my submit script or executable script,
and I post them in my previous message.
How should I correct my script?
Hsin-Lin
Hi,
how many CPUs do you try to use? How big is your system. What kind of
interconnect? Since you use condor probably some pretty slow interconnect.
Than you can't aspect it to work on many CPUs. If you want to use many CPUs
for MD you need a faster interconnect.
Roland
2010/4/2 Hsin-Lin Chiang jian...@phys.sinica.edu.tw
#160;Hi,
Do someone use gromacs, lam, and condor together here?
I use gromacs with lam/mpi on condor system.
Everytime I submit the parallel job.
I got the node which is occupied before and the performance of each cpu is
below 10%.
How should I change the script?
Below is one submit script and two executable script.
condor_mpi:
#!/bin/bash
Universe = parallel
Executable = ./lamscript
machine_count = 8
output = md_$(NODE).out
error = md_$(NODE).err
log = md.log
arguments = /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md.sh
+WantIOProxy = True
should_transfer_files = yes
when_to_transfer_output = on_exit
Queue
---
lamscript:
---
#!/bin/sh
_CONDOR_PROCNO=$_CONDOR_PROCNO
_CONDOR_NPROCS=$_CONDOR_NPROCS
_CONDOR_REMOTE_SPOOL_DIR=$_CONDOR_REMOTE_SPOOL_DIR
SSHD_SH=`condor_config_val libexec`
SSHD_SH=$SSHD_SH/sshd.sh
CONDOR_SSH=`condor_config_val libexec`
CONDOR_SSH=$CONDOR_SSH/condor_ssh
# Set this to the bin directory of your lam installation
# This also must be in your .cshrc file, so the remote side
# can find it!
export LAMDIR=/stathome/jiangsl/soft/lam-7.1.4
export PATH=${LAMDIR}/bin:${PATH}
export LD_LIBRARY_PATH=/lib:/usr/lib:$LAMDIR/lib:.:/opt/intel/compilers/lib
. $SSHD_SH $_CONDOR_PROCNO $_CONDOR_NPROCS
# If not the head node, just sleep forever, to let the
# sshds run
if [ $_CONDOR_PROCNO -ne 0 ]
then
#160; #160; #160; #160; #160; #160; #160; #160; wait
#160; #160; #160; #160; #160; #160; #160; #160; sshd_cleanup
#160; #160; #160; #160; #160; #160; #160; #160; exit 0
fi
EXECUTABLE=$1
shift
# the binary is copied but the executable flag is cleared.
# so the script have to take care of this
chmod +x $EXECUTABLE
# to allow multiple lam jobs running on a single machine,
# we have to give somewhat unique value
export LAM_MPI_SESSION_SUFFIX=$$
export LAMRSH=$CONDOR_SSH
# when a job is killed by the user, this script will get sigterm
# This script have to catch it and do the cleaning for the
# lam environment
finalize()
{
sshd_cleanup
lamhalt
exit
}
trap finalize TERM
CONDOR_CONTACT_FILE=$_CONDOR_SCRATCH_DIR/contact
export $CONDOR_CONTACT_FILE
# The second field in the contact file is the machine name
# that condor_ssh knows how to use. Note that this used to
# say sort -n +0 ..., but -n option is now deprecated.
sort $CONDOR_CONTACT_FILE | awk '{print $2}' machines
# start the lam environment
# For older versions of lam you may need to remove the -ssi boot rsh line
lamboot -ssi boot rsh -ssi rsh_agent $LAMRSH -x machines
if [ $? -ne 0 ]
then
#160; #160; #160; #160; echo lamscript error booting lam
#160; #160; #160; #160; exit 1
fi
mpirun C -ssi rpi usysv -ssi coll_smp 1 $EXECUTABLE $@
CHILD=$!
TMP=130
while [ $TMP -gt 128 ] ; do
#160; #160; #160; #160; wait $CHILD
#160; #160; #160; #160; TMP=$?;
done
# clean up files
sshd_cleanup
/bin/rm -f machines
# clean up lam
lamhalt
exit $TMP
md.sh
#!/bin/sh
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.0.5/bin/mdrun_mpi_d \
-s /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.tpr \
-e /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.edr \
-o /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.trr \
-g /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.log \
-c /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.gro
-
Hsin-Lin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 72, Issue 13
Hi,
I tried to use 4 and 8 CPUs.
There are about 6000 atoms in my system.
The interconnect of our computer is the network with speed 1Gb but not optical
fiber.
I'm sorry for my poor English and I couldn't express well in my question.
Everytime I submitted the parallel job, the nodes assigned to mehave been 100%
loading,
and the CPU source availble to me is less then 10%.
I think there is something wrong with my submit script or executable script,
so I post them in my question before.(please see those below)
Hsin-Lin
Hi,
how many CPUs do you try to use? How big is your system. What kind of
interconnect? Since you use condor probably some pretty slow interconnect.
Than you can't aspect it to work on many CPUs. If you want to use many CPUs
for MD you need a faster interconnect.
Roland
2010/4/2 Hsin-Lin Chiang jian...@phys.sinica.edu.tw
#160;Hi,
Do someone use gromacs, lam, and condor together here?
I use gromacs with lam/mpi on condor system.
Everytime I submit the parallel job.
I got the node which is occupied before and the performance of each cpu is
below 10%.
How should I change the script?
Below is one submit script and two executable script.
condor_mpi:
#!/bin/bash
Universe = parallel
Executable = ./lamscript
machine_count = 2
output = md_$(NODE).out
error = md_$(NODE).err
log = md.log
arguments = /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md.sh
+WantIOProxy = True
should_transfer_files = yes
when_to_transfer_output = on_exit
Queue
---
lamscript:
---
#!/bin/sh
_CONDOR_PROCNO=$_CONDOR_PROCNO
_CONDOR_NPROCS=$_CONDOR_NPROCS
_CONDOR_REMOTE_SPOOL_DIR=$_CONDOR_REMOTE_SPOOL_DIR
SSHD_SH=`condor_config_val libexec`
SSHD_SH=$SSHD_SH/sshd.sh
CONDOR_SSH=`condor_config_val libexec`
CONDOR_SSH=$CONDOR_SSH/condor_ssh
# Set this to the bin directory of your lam installation
# This also must be in your .cshrc file, so the remote side
# can find it!
export LAMDIR=/stathome/jiangsl/soft/lam-7.1.4
export PATH=${LAMDIR}/bin:${PATH}
export LD_LIBRARY_PATH=/lib:/usr/lib:$LAMDIR/lib:.:/opt/intel/compilers/lib
. $SSHD_SH $_CONDOR_PROCNO $_CONDOR_NPROCS
# If not the head node, just sleep forever, to let the
# sshds run
if [ $_CONDOR_PROCNO -ne 0 ]
then
#160; #160; #160; #160; #160; #160; #160; #160; wait
#160; #160; #160; #160; #160; #160; #160; #160; sshd_cleanup
#160; #160; #160; #160; #160; #160; #160; #160; exit 0
fi
EXECUTABLE=$1
shift
# the binary is copied but the executable flag is cleared.
# so the script have to take care of this
chmod +x $EXECUTABLE
# to allow multiple lam jobs running on a single machine,
# we have to give somewhat unique value
export LAM_MPI_SESSION_SUFFIX=$$
export LAMRSH=$CONDOR_SSH
# when a job is killed by the user, this script will get sigterm
# This script have to catch it and do the cleaning for the
# lam environment
finalize()
{
sshd_cleanup
lamhalt
exit
}
trap finalize TERM
CONDOR_CONTACT_FILE=$_CONDOR_SCRATCH_DIR/contact
export $CONDOR_CONTACT_FILE
# The second field in the contact file is the machine name
# that condor_ssh knows how to use. Note that this used to
# say sort -n +0 ..., but -n option is now deprecated.
sort $CONDOR_CONTACT_FILE | awk '{print $2}' machines
# start the lam environment
# For older versions of lam you may need to remove the -ssi boot rsh line
lamboot -ssi boot rsh -ssi rsh_agent $LAMRSH -x machines
if [ $? -ne 0 ]
then
#160; #160; #160; #160; echo lamscript error booting lam
#160; #160; #160; #160; exit 1
fi
mpirun C -ssi rpi usysv -ssi coll_smp 1 $EXECUTABLE $@
CHILD=$!
TMP=130
while [ $TMP -gt 128 ] ; do
#160; #160; #160; #160; wait $CHILD
#160; #160; #160; #160; TMP=$?;
done
# clean up files
sshd_cleanup
/bin/rm -f machines
# clean up lam
lamhalt
exit $TMP
md.sh
#!/bin/sh
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.0.5/bin/mdrun_mpi_d \
-s /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.tpr \
-e /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.edr \
-o /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.trr \
-g /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.log \
-c /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.gro
-
Hsin-Lin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs, lam and condor
Hi,
Do someone use gromacs, lam, and condor together here?
I use gromacs with lam/mpi on condor system.
Everytime I submit the parallel job.
I got the node which is occupied before and the performance of each cpu is
below 10%.
How should I change the script?
Below is one submit script and two executable script.
condor_mpi:
#!/bin/bash
Universe = parallel
Executable = ./lamscript
machine_count = 2
output = md_$(NODE).out
error = md_$(NODE).err
log = md.log
arguments = /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md.sh
+WantIOProxy = True
should_transfer_files = yes
when_to_transfer_output = on_exit
Queue
---
lamscript:
---
#!/bin/sh
_CONDOR_PROCNO=$_CONDOR_PROCNO
_CONDOR_NPROCS=$_CONDOR_NPROCS
_CONDOR_REMOTE_SPOOL_DIR=$_CONDOR_REMOTE_SPOOL_DIR
SSHD_SH=`condor_config_val libexec`
SSHD_SH=$SSHD_SH/sshd.sh
CONDOR_SSH=`condor_config_val libexec`
CONDOR_SSH=$CONDOR_SSH/condor_ssh
# Set this to the bin directory of your lam installation
# This also must be in your .cshrc file, so the remote side
# can find it!
export LAMDIR=/stathome/jiangsl/soft/lam-7.1.4
export PATH=${LAMDIR}/bin:${PATH}
export LD_LIBRARY_PATH=/lib:/usr/lib:$LAMDIR/lib:.:/opt/intel/compilers/lib
. $SSHD_SH $_CONDOR_PROCNO $_CONDOR_NPROCS
# If not the head node, just sleep forever, to let the
# sshds run
if [ $_CONDOR_PROCNO -ne 0 ]
then
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
wait
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
sshd_cleanup
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
exit 0
fi
EXECUTABLE=$1
shift
# the binary is copied but the executable flag is cleared.
# so the script have to take care of this
chmod +x $EXECUTABLE
# to allow multiple lam jobs running on a single machine,
# we have to give somewhat unique value
export LAM_MPI_SESSION_SUFFIX=$$
export LAMRSH=$CONDOR_SSH
# when a job is killed by the user, this script will get sigterm
# This script have to catch it and do the cleaning for the
# lam environment
finalize()
{
sshd_cleanup
lamhalt
exit
}
trap finalize TERM
CONDOR_CONTACT_FILE=$_CONDOR_SCRATCH_DIR/contact
export $CONDOR_CONTACT_FILE
# The second field in the contact file is the machine name
# that condor_ssh knows how to use. Note that this used to
# say sort -n +0 ..., but -n option is now deprecated.
sort $CONDOR_CONTACT_FILE | awk '{print $2}' machines
# start the lam environment
# For older versions of lam you may need to remove the -ssi boot rshline
lamboot -ssi boot rsh -ssi rsh_agent $LAMRSH -x machines
if [ $? -ne 0 ]
then
#160;#160;#160;#160;#160;#160;#160; echo lamscript error booting lam
#160;#160;#160;#160;#160;#160;#160; exit 1
fi
mpirun C -ssi rpi usysv -ssi coll_smp 1 $EXECUTABLE $@
CHILD=$!
TMP=130
while [ $TMP -gt 128 ] ; do
#160;#160;#160;#160;#160;#160;#160; wait $CHILD
#160;#160;#160;#160;#160;#160;#160; TMP=$?;
done
# clean up files
sshd_cleanup
/bin/rm -f machines
# clean up lam
lamhalt
exit $TMP
md.sh
#!/bin/sh
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.0.5/bin/mdrun_mpi_d \
-s /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.tpr \
-e /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.edr \
-o /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.trr \
-g /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.log \
-c /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.gro
-
Hsin-Lin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
