Re: [gmx-users] using more processors for g_mindist
Mark, i want to know which water atoms stay within a cut off to protein atom. ie i need the duration at which a water resides on the protein atoms. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 6:01 PM, aiswarya pawar wrote: Mark, Right now am computing distance between each protein atom against all water atoms, That's expensive. mdrun goes to great lengths to speed up computing billions of distances. which is taking too long for 5ns run. i cant reduce the frames Yes you can. Even if you think you need data from every frame, you probably don't because they're correlated with each other, and at the very least you can do a pilot study on a frame every 100ps or every nanosecond before committing to one on all the frames. either the number of water atoms. So is there any alternate. You are not likely to get a better solution if you only describe your attempt, rather than describe the objective. Asking how do I hammer harder? if you're hammering a screw makes it impossible to get the correct solution Use a screwdriver. Mark Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? No. If it will take too long, you need to reduce your number of frames (trjconv), or the number of atoms (also trjconv), or some such. Mark and will this effect the output in anyways. Thanks, -- Aiswarya B Pawar -- 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 -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] error
Dear friends, iam doing protein-ligand dynamics and i have completed everything.iam running for 2ns. After submitting to cluster,i am getting the error as File input/output error: Cannot rename checkpoint file; maybe you are out of quota? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please help me how to solve this error -- *Ramya.LN* -- *Ramya.LN* -- 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] using more processors for g_mindist
On 29/02/2012 7:21 PM, aiswarya pawar wrote: Mark, i want to know which water atoms stay within a cut off to protein atom. OK, but as you will read in g_mindist -h, it will count such atoms and not identify which they were... ie i need the duration at which a water resides on the protein atoms. ... and identity of the atoms is needed for measuring duration of contact. g_dist does something like this, and reading g_mindist -h should have prompted you to find this out. Otherwise, you will have to construct an index group for each water molecule, and script a loop to examine each water molecule separately using some tool that observes what you really want to measure. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. You also need to be clear about whether you care about continuous contact. Does a water molecule that oscillates at a distance around the cutoff reside about 50% of the time? You still don't need high time resolution for testing whether this analysis might give you the information you want. The water molecules that are in contact for more than 50% of the time (continuous or not) will show up in 5 snapsnots spaced every nanosecond. 5000 snapshots every picosecond is better, but not if you can't afford to wait for it. Mark Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 29/02/2012 6:01 PM, aiswarya pawar wrote: Mark, Right now am computing distance between each protein atom against all water atoms, That's expensive. mdrun goes to great lengths to speed up computing billions of distances. which is taking too long for 5ns run. i cant reduce the frames Yes you can. Even if you think you need data from every frame, you probably don't because they're correlated with each other, and at the very least you can do a pilot study on a frame every 100ps or every nanosecond before committing to one on all the frames. either the number of water atoms. So is there any alternate. You are not likely to get a better solution if you only describe your attempt, rather than describe the objective. Asking how do I hammer harder? if you're hammering a screw makes it impossible to get the correct solution Use a screwdriver. Mark Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? No. If it will take too long, you need to reduce your number of frames (trjconv), or the number of atoms (also trjconv), or some such. Mark and will this effect the output in anyways. Thanks, -- Aiswarya B Pawar -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error
On 29/02/2012 7:28 PM, RAMYA NAGA wrote: Dear friends, iam doing protein-ligand dynamics and i have completed everything.iam running for 2ns. After submitting to cluster,i am getting the error as File input/output error: Cannot rename checkpoint file; maybe you are out of quota? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors There is some problem with your filesystem thinking the files are not available. Perhaps some old calculation is still running using it. Perhaps you do not have write permission for your directory. Maybe (your part of) the filesystem is full. We can only guess. 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] Gromacs-GPU benchmark test killed after exhausting the memory
Hi, I have Gromacs-GPU version 4.5.5 and GTX 580. I ran dhfr-solv-PME benchmark test (see below) and my run was killed after couple of hours exhausting all the computer memory, including the swap (2G + 4G swap). Has anyone encountered this problem? What is wrong? Thanks, Efrat mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes -deffnm md :-) G R O M A C S (-: Great Red Oystrich Makes All Chemists Sane :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun-gpu (-: Option Filename Type Description -s md.tpr InputRun input file: tpr tpb tpa -o md.trr Output Full precision trajectory: trr trj cpt -x md.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi md.cpt Input, Opt. Checkpoint file -cpo md.cpt Output, Opt. Checkpoint file -c md.gro Output Structure file: gro g96 pdb etc. -e md.edr Output Energy file -g md.log Output Log file -dhdlmd.xvg Output, Opt. xvgr/xmgr file -field md.xvg Output, Opt. xvgr/xmgr file -table md.xvg Input, Opt. xvgr/xmgr file -tablep md.xvg Input, Opt. xvgr/xmgr file -tableb md.xvg Input, Opt. xvgr/xmgr file -rerun md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi md.xvg Output, Opt. xvgr/xmgr file -tpidmd.xvg Output, Opt. xvgr/xmgr file -ei md.edi Input, Opt. ED sampling input -eo md.edo Output, Opt. ED sampling output -j md.gct Input, Opt. General coupling stuff -jo md.gct Output, Opt. General coupling stuff -ffout md.xvg Output, Opt. xvgr/xmgr file -devout md.xvg Output, Opt. xvgr/xmgr file -runav md.xvg Output, Opt. xvgr/xmgr file -px md.xvg Output, Opt. xvgr/xmgr file -pf md.xvg Output, Opt. xvgr/xmgr file -mtx md.mtx Output, Opt. Hessian matrix -dn md.ndx Output, Opt. Index file -multidirmd Input, Opt., Mult. Run directory Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -deffnm string md Set the default filename for all file options -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -gcomint-1 Global communication frequency -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 15 Checkpoint interval (minutes) -[no]cpnum bool no Keep and number checkpoint files -[no]append bool yes Append to
Re: [gmx-users] Re: gmx-users Digest, Vol 94, Issue 185
conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distributionchanged gen_temp= 400; temperature for Maxwell distribution gen_seed= 100; generate a random seed ld_seed=-1 Thank you! Bo -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 2 Date: Wed, 29 Feb 2012 12:48:05 +1100 From: Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Subject: Re: [gmx-users] change simulation temperature To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 769090a715160.4f4e1...@anu.edu.au mailto:769090a715160.4f4e1...@anu.edu.au Content-Type: text/plain; charset=us-ascii On 29/02/12, bo.shuang b...@rice.edu mailto:b...@rice.edu wrote: Hi, all, I have a question about change the temperature in simulation. When I change the ref_t and gen_temp only, (from 300 to 400) I cannot see any difference. I am thinking if I need to change tau_t also, since diffusivity constant is also related to temperature. Am I right? Here is my mdp file: title= OPLS Lysozyme NVT equilibration ;define= -DPOSRES; position restrain the protein ; Run parameters integrator= bd; leap-frog integrator By their nature, Browning and stochastic dynamics do not work with temperature coupling algorithms. IIRC gen_temp + gen_vel should have an effect on the initial conditions. Mark nsteps= 50; 2 * 50 = 1000 ps dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps ; Bond parameters continuation= yes; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= system; two coupling groups - more accurate tau_t= 0.01; time constant, in ps ref_t= 400 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no ; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distributionchanged gen_temp= 400; temperature for Maxwell distribution gen_seed= 100; generate a random seed ld_seed=-1 Thank you! Bo -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120229/c93c41c8/attachment-0001.html -- Message: 3 Date: Tue, 28 Feb 2012 18:19:16 -0800 (PST) From: Adam Jion adamj...@yahoo.com mailto:adamj...@yahoo.com Subject: [gmx-users] NaN error using mdrun-gpu To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 1330481956.42489.yahoomail...@web30606.mail.mud.yahoo.com mailto:1330481956.42489.yahoomail...@web30606.mail.mud.yahoo.com Content-Type: text/plain
RE: [gmx-users] error
try: $ df -h . And see how much quota you have available. Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of RAMYA NAGA [nagra...@gmail.com] Sent: Wednesday, February 29, 2012 8:28 AM To: Discussion list for GROMACS users Subject: [gmx-users] error Dear friends, iam doing protein-ligand dynamics and i have completed everything.iam running for 2ns. After submitting to cluster,i am getting the error as File input/output error: Cannot rename checkpoint file; maybe you are out of quota? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please help me how to solve this error -- Ramya.LN -- Ramya.LN -- 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] using more processors for g_mindist
Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist 5.00e+02 518 42680 5.01e+02 518 20942 5.02e+02 518 67844 5.03e+02 518 5984 5.04e+02 518 67844 5.05e+02 518 5984 5.06e+02 518 30116 5.07e+02 518 67844 5.08e+02 518 32957 5.09e+02 518 67844 5.10e+02 518 19610 5.11e+02 518 19610 5.12e+02 518 22895 5.13e+02 518 30116 5.14e+02 518 19610 5.15e+02 518 22895 5.16e+02 518 13628 5.17e+02 518 5984 2nd column is the protein atom and the 3rd column the water atom. if iam doing g_dist how is it possible to know the which water molecule has to be considered for the distance calculations ie should i compute the distance between one protein atom against all the water within the cut off individually? Thanks On Wed, Feb 29, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 7:21 PM, aiswarya pawar wrote: Mark, i want to know which water atoms stay within a cut off to protein atom. OK, but as you will read in g_mindist -h, it will count such atoms and not identify which they were... ie i need the duration at which a water resides on the protein atoms. ... and identity of the atoms is needed for measuring duration of contact. g_dist does something like this, and reading g_mindist -h should have prompted you to find this out. Otherwise, you will have to construct an index group for each water molecule, and script a loop to examine each water molecule separately using some tool that observes what you really want to measure. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. You also need to be clear about whether you care about continuous contact. Does a water molecule that oscillates at a distance around the cutoff reside about 50% of the time? You still don't need high time resolution for testing whether this analysis might give you the information you want. The water molecules that are in contact for more than 50% of the time (continuous or not) will show up in 5 snapsnots spaced every nanosecond. 5000 snapshots every picosecond is better, but not if you can't afford to wait for it. Mark Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 6:01 PM, aiswarya pawar wrote: Mark, Right now am computing distance between each protein atom against all water atoms, That's expensive. mdrun goes to great lengths to speed up computing billions of distances. which is taking too long for 5ns run. i cant reduce the frames Yes you can. Even if you think you need data from every frame, you probably don't because they're correlated with each other, and at the very least you can do a pilot study on a frame every 100ps or every nanosecond before committing to one on all the frames. either the number of water atoms. So is there any alternate. You are not likely to get a better solution if you only describe your attempt, rather than describe the objective. Asking how do I hammer harder? if you're hammering a screw makes it impossible to get the correct solution Use a screwdriver. Mark Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? No. If it will take too long, you need to reduce your number of frames (trjconv), or the number of atoms (also trjconv), or some such. Mark and will this effect the output in anyways. Thanks, -- Aiswarya B Pawar -- 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 -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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
Re: [gmx-users] Implicit solvent - Gromacs 4.5.4
On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: I run energy minimization of my protein with implicit solvent: constraints = none integrator = steep dt = 0.001 ; ps nsteps = 3 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb = 0 rvdw = 0 comm-mode = angular comm-grps = Protein optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 5.0 emstep = 0.01 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1 rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.25936 And I obtained: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 3 Step Time Lambda 0 0.0 0.0 Steepest Descents converged to Fmax 1000 in 1 steps Potential Energy = inf Maximum force = 0.000e+00 on atom 0 Norm of force = nan Can you please explain? Not without more information. 1. What is in the system? - protein without specified box 2. Which version of Gromacs is this?- Gromacs 4.5.4 3. Are you using GPU or CPU architecture? - I run it straight from the cluster on a specific node Doesn't answer the question, but I'll assume CPU since EM doesn't work on GPU's. Just checking. 4. Does an in vacuo minimization work (i.e., just turn off the GB parts)? - yes, it works And what is the output? In any case, I can't reproduce any problem doing EM with implicit solvent in 4.5.4 - my test systems work quite well. It may just be that the system cannot be minimized because of some clash that is unfavorable in an implicit solvent environment (thus causing an immediate halt, though that would be odd) but can be resolved in vacuo. Try using the structure produced by in vacuo minimization as input into the implicit solvent EM to see if this may be the case. What shoould be the value for emtol in implicit solvent model with protein with app. 150 residues? One that is sufficient for the inherent forces in the system and for your application ;) I don't think there are any hard and fast rules here for standard MD, and the target is not dictated by the size of the protein. -Justin Thank you Justin. Mark, would you suggest equilibration e.g. for 1ns with no restraints and no constraints in implicic solvent with timestep =0.0005 and then run MD with implicit employing LINCS? Steven -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] using g_angle
Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is instead to know the value in degrees of each angle in the ndx file. Do you have any suggestions apart from building an index file for each angle? Thanks Francesca -- 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] Positive Coul. recip. term
On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote: The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and the force field is from Lopes (CLaP). I tried deleting all of the cation dihedrals from the itp file and found that the run did not crash, although it still had a positive coul recip term. Upon examination of the cation dihedrals I noticed that there was a typo in which a set of unbonded carbons were put together in a dihedral term. Perhaps this is what made the previous runs crash. Even with this correction, the coul. recip. term is still positive. I have tried smaller time steps and changing ewald_tol to 1e-3, but these have not resolved this issue. How can I calculate the error in the electrostatic force? Denny The error of PME can be estimated a priori with the tool g_pme_error. I would suggest to tune it to a bound below 1e-3. I took a look at the force field parameters for the pyrrolidinium, which is published by Lopes in 2006, and I assume you use this parameters, are you ? I do not understand Table I in this paper. The dihedral parameters are just given for V_2 and V_4, and for a certain dihedral they are even set to zero. If you use this force field, how are the other parameters obtained ? Are they zero or do they correspond to the OPLS values given in the reference cited on the top of the table ? /Flo On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote: Thank you both for your replies. I currently have another ionic liquid running just fine on the same gromacs build (compiled the tpr file yesterday), so I am reluctant to conclude that the problem is with the linking. Please let me know if you disagree. The force field I am using was published in 2004 and has been validated by another group. I have double and triple checked my itp files to make sure they match the force field, but it's possible there are still some errors there. Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who validated it, I am just curious, and what is the ionic liquid ? Though you are constraining the hbonds, I would be cautious with the time step of 2fs, because it might be, that the eigenfrequency of the anionic bonds requires a shorter time step, but this should not be the problem of a positive Coulomb energy. Have you calculated the error in the electrostatic force ? I would suggest to tune it to a limit of 1e-3, perhaps this resolves the problem of the positive Coulomb term. Perhaps some 1--4 and dihedral interactions are missing in the itp file, so assure if all of them are provided correctly. /Flo I agree that this is very strange and feel that there must be something fundamentally wrong in the mdp file or deeper. I have included my mdp file below. title = PMP+TFN cpp = /lib/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 1000 ; total 20 ns nstcomm = 10 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = Cut-off rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = v-rescale tc_grps = PMP TFN tau_t = 0.2 0.2 ref_t = 300 300 nsttcouple = 1 ; Energy monitoring energygrps = PMP TFN ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed
[gmx-users] quick question about restart
Dear gmx-users, I'm running my simulations on a machine with a queue system that stops the runs longer than 24 hours. Often, for my simulations, I need a longer time to complete the runs. Let's have an example. I have to run a 100ns-long simulation on a machine that produces 10ns/days simulation. I have two possibilities: First approach: I'm setting within the .mdp file a global duration of 100 ns. Then: grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, I see that the run has been stopped after 10 ns. I have the output_fullMD.cpt file. Then, I do: mdrun -s input_fullMD.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the run has been completed (then I will concatenate the .xtc, .edr, .trr files) Second approach: I'm setting within the .mdp file a global duration of 10 ns. Then (as above): grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, the run has been finished. Then, I continue the run for other 10 ns with: tpbconv -s input_fullMD.tpr -extend 1 -o input_fullMD_2.tpr mdrun -s input_fullMD_2.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the 100-ns run has been completed. Are the two procedure producing EXACTLY the same results, or not? Which is the best preferred procedure? Thank you very much Anna Anna Marabotti, Ph.D. Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man (Roberto Benigni, about Roberto Saviano) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Implicit solvent - Gromacs 4.5.4
On 29/02/2012 9:26 PM, Steven Neumann wrote: On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: I run energy minimization of my protein with implicit solvent: constraints = none integrator = steep dt = 0.001 ; ps nsteps = 3 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb = 0 rvdw = 0 comm-mode = angular comm-grps = Protein optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 5.0 emstep = 0.01 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1 rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.25936 And I obtained: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 3 Step Time Lambda 0 0.0 0.0 Steepest Descents converged to Fmax 1000 in 1 steps Potential Energy = inf Maximum force = 0.000e+00 on atom 0 Norm of force = nan Can you please explain? Not without more information. 1. What is in the system? - protein without specified box 2. Which version of Gromacs is this?- Gromacs 4.5.4 3. Are you using GPU or CPU architecture? - I run it straight from the cluster on a specific node Doesn't answer the question, but I'll assume CPU since EM doesn't work on GPU's. Just checking. 4. Does an in vacuo minimization work (i.e., just turn off the GB parts)? - yes, it works And what is the output? In any case, I can't reproduce any problem doing EM with implicit solvent in 4.5.4 - my test systems work quite well. It may just be that the system cannot be minimized because of some clash that is unfavorable in an implicit solvent environment (thus causing an immediate halt, though that would be odd) but can be resolved in vacuo. Try using the structure produced by in vacuo minimization as input into the implicit solvent EM to see if this may be the case. What shoould be the value for emtol in implicit solvent model with protein with app. 150 residues? One that is sufficient for the inherent forces in the system and for your application ;) I don't think there are any hard and fast rules here for standard MD, and the target is not dictated by the size of the protein. -Justin Thank you Justin. Mark, would you suggest equilibration e.g. for 1ns with no restraints and no constraints in implicic solvent with timestep =0.0005 and then run MD with implicit employing LINCS? I have suggested such equilibration protocols in the past for implicit solvent - maybe 1ns is excessive. I've had simple peptide systems with no atomic clashes that have wanted such gentle treatment. 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] quick question about restart
On 29/02/2012 9:47 PM, Anna Marabotti wrote: Dear gmx-users, I'm running my simulations on a machine with a queue system that stops the runs longer than 24 hours. Often, for my simulations, I need a longer time to complete the runs. Let's have an example. I have to run a 100ns-long simulation on a machine that produces 10ns/days simulation. I have two possibilities: First approach: I'm setting within the .mdp file a global duration of 100 ns. Then: grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, I see that the run has been stopped after 10 ns. I have the output_fullMD.cpt file. Then, I do: mdrun -s input_fullMD.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the run has been completed (then I will concatenate the .xtc, .edr, .trr files) Yep, or use the same -deffnm filename and -append for more simplicity. See http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#section_2 Second approach: I'm setting within the .mdp file a global duration of 10 ns. Then (as above): grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, the run has been finished. Then, I continue the run for other 10 ns with: tpbconv -s input_fullMD.tpr -extend 1 -o input_fullMD_2.tpr mdrun -s input_fullMD_2.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the 100-ns run has been completed. Are the two procedure producing EXACTLY the same results, or not? In principle, they are implementing the same algorithm over the 10 runs. In practice, the discussion at http://www.gromacs.org/Documentation/Terminology/Reproducibility applies and you will likely not observe an identical trajectory from each case. In theory, mdrun -reprod does a better job in many cases for often losing performance, but random number states are not preserved, so various algorithms cannot be reproducible across restarts. Which is the best preferred procedure? The first, with appending, is simple and requires no concatenation post-processing. Feel free to back up your files between runs if you want insurance against loss - but you should do that anyway. Anything else requires you to do more work later on for no gain. 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] using g_angle
On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is instead to know the value in degrees of each angle in the ndx file. Do you have any suggestions apart from building an index file for each angle? g_angle -ov -all with each angle in its own group. 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] using more processors for g_mindist
On 29/02/2012 9:05 PM, aiswarya pawar wrote: Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist What makes you think there is only one atom satisfying that cutoff? 5.00e+02 518 42680 5.01e+02 518 20942 5.02e+02 518 67844 5.03e+02 518 5984 5.04e+02 518 67844 5.05e+02 518 5984 5.06e+02 518 30116 5.07e+02 518 67844 5.08e+02 518 32957 5.09e+02 518 67844 5.10e+02 518 19610 5.11e+02 518 19610 5.12e+02 518 22895 5.13e+02 518 30116 5.14e+02 518 19610 5.15e+02 518 22895 5.16e+02 518 13628 5.17e+02 518 5984 2nd column is the protein atom and the 3rd column the water atom. Chunk of output from an unnamed file without giving the command line that generated it is close to useless :-) Anyway, whatever information is present here is not helping you observe the duration of a contact between the protein and any given water molecule. if iam doing g_dist how is it possible to know the which water molecule has to be considered for the distance calculations ie should i compute the distance between one protein atom against all the water within the cut off individually? If you have read g_dist -h and want to ask this question, then I did not understand your previous statement of your objective. Mark Thanks On Wed, Feb 29, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 29/02/2012 7:21 PM, aiswarya pawar wrote: Mark, i want to know which water atoms stay within a cut off to protein atom. OK, but as you will read in g_mindist -h, it will count such atoms and not identify which they were... ie i need the duration at which a water resides on the protein atoms. ... and identity of the atoms is needed for measuring duration of contact. g_dist does something like this, and reading g_mindist -h should have prompted you to find this out. Otherwise, you will have to construct an index group for each water molecule, and script a loop to examine each water molecule separately using some tool that observes what you really want to measure. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. You also need to be clear about whether you care about continuous contact. Does a water molecule that oscillates at a distance around the cutoff reside about 50% of the time? You still don't need high time resolution for testing whether this analysis might give you the information you want. The water molecules that are in contact for more than 50% of the time (continuous or not) will show up in 5 snapsnots spaced every nanosecond. 5000 snapshots every picosecond is better, but not if you can't afford to wait for it. Mark Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 29/02/2012 6:01 PM, aiswarya pawar wrote: Mark, Right now am computing distance between each protein atom against all water atoms, That's expensive. mdrun goes to great lengths to speed up computing billions of distances. which is taking too long for 5ns run. i cant reduce the frames Yes you can. Even if you think you need data from every frame, you probably don't because they're correlated with each other, and at the very least you can do a pilot study on a frame every 100ps or every nanosecond before committing to one on all the frames. either the number of water atoms. So is there any alternate. You are not likely to get a better solution if you only describe your attempt, rather than describe the objective. Asking how do I hammer harder? if you're hammering a screw makes it impossible to get the correct solution Use a screwdriver. Mark Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? No. If it will take too long, you need to reduce your number of frames (trjconv), or the number of atoms (also trjconv), or some
Re: [gmx-users] md in vacuo
On 29/02/2012 8:33 PM, Thomas Evangelidis wrote: Dear GROMACS community, I use the following parameters to run MD of ethane in vacuo. Then I calculate the H-C-C-H dihedral angle distribution and from that the rotational energy barrier using the formula DeltG=-k*T*ln(x), where x is the dihedral value. The rotational energy barrier is correct (~ 12 kJ) with all-bond constraints, but not with h-bond or no bond constraints. Could anyone tell me which other parameters to tweak in order to get the correct dihedral angle distribution without any bond constraints. Thanks in advance. Thomas integrator = md tinit= 0.0 dt = 0.002 This is too long if you are not using all-atom constraints. See manual 6.5 for discussion. Mark nsteps = 250 init_step= 0 simulation_part = 1 comm-mode= Angular nstcomm = 20 comm-grps= emtol= 0.01 emstep = 0.01 niter= 0 fcstep = 0 nstcgsteep = 1000 nbfgscorr= 10 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstcalcenergy= -1 nstenergy= 500 nstxtcout= 100 xtc-precision= 1000 xtc-grps = energygrps = System nstlist = 0 ns_type = simple pbc = no periodic_molecules = no rlist= 0 rlistlong= -1 coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 0.0 epsilon_r= 1.0 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 0 DispCorr = no table-extension = 1 energygrp_table = implicit_solvent = No tcoupl = v-rescale nsttcouple = 5 nh-chain-length = 10 tc-grps = System tau_t= 0.1 ref_t= 300 Pcoupl = no Pcoupltype = Isotropic nstpcouple = -1 tau_p= 1 compressibility = ref_p= 1.01.01.0 refcoord_scaling = No andersen_seed= 815131 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR= no shake-tol= 1e-04 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 morse= no -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr mailto:tev...@bioacademy.gr teva...@gmail.com mailto:teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] using g_angle
2012/2/29 Mark Abraham mark.abra...@anu.edu.au: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. Actually mk_angndx gies me the angles for phi and psi while instead I need omega and they are put in a strange format like in groups of 8 instead of 4. However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is instead to know the value in degrees of each angle in the ndx file. Do you have any suggestions apart from building an index file for each angle? g_angle -ov -all with each angle in its own group. What do you mean with each angle in its own group? something like [dihedrals] 2 5 9 10 [dihedrals] 10 13 16 18 ... Isn't it equivalent to build differend index files? anyway the -ov flag gives the average over time, but I need the angles just at one time, that is why I was using -od but it just plots the distribution of all angles together. Any help? Thanks Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using g_angle
hi francesca, i think what you are looking for is this g_sgangle $indexFile -f $traj -s $tpr -oa $outfile before that, you have to define two planes (by 3 atom indices each) in your index file [ dihed1 ] 523 680 3482 [ dihed2 ] 680 3482 3691 which you choose when having started g_sgangle. the most important part is the -oa option!! what you get then is something like ... #@title Angle between dihed1 and dihed2 #@xaxis label Time (ps) #@yaxis label Angle (degrees) #@TYPE xy 00.9226 22.6908 0.4 0.930216 21.5314 0.8 0.930954 21.4159 1.2 0.927077 22.0163 1.6 0.935084 20.7583 2 0.933544 21.0059 2.4 0.92863521.777 2.8 0.916627 23.5621 3.2 0.923862 22.5027 ... ciao vedat Am 29.02.2012 13:54, schrieb francesca vitalini: 2012/2/29 Mark Abrahammark.abra...@anu.edu.au: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. Actually mk_angndx gies me the angles for phi and psi while instead I need omega and they are put in a strange format like in groups of 8 instead of 4. However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is instead to know the value in degrees of each angle in the ndx file. Do you have any suggestions apart from building an index file for each angle? g_angle -ov -all with each angle in its own group. What do you mean with each angle in its own group? something like [dihedrals] 2 5 9 10 [dihedrals] 10 13 16 18 ... Isn't it equivalent to build differend index files? anyway the -ov flag gives the average over time, but I need the angles just at one time, that is why I was using -od but it just plots the distribution of all angles together. Any help? Thanks 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 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] using g_angle
On 29/02/2012 11:54 PM, francesca vitalini wrote: 2012/2/29 Mark Abrahammark.abra...@anu.edu.au: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. Actually mk_angndx gies me the angles for phi and psi while instead I need omega and they are put in a strange format like in groups of 8 instead of 4. Whitespace inside the index group probably doesn't matter. However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is instead to know the value in degrees of each angle in the ndx file. Do you have any suggestions apart from building an index file for each angle? g_angle -ov -all with each angle in its own group. What do you mean with each angle in its own group? something like [dihedrals] 2 5 9 10 [dihedrals] 10 13 16 18 ... Yes, but with unique group names - but it turns out I was wrong to suggest that. Your index file above is fine. Isn't it equivalent to build differend index files? anyway the -ov flag gives the average over time, but I need the angles just at one time, that is why I was using -od but it just plots the distribution of all angles together. Any help? Which part of the output of g_angle -ov **-all** doesn't suit you? Mark Thanks 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun -pd
On 1/03/2012 12:31 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to use option -p of mdrun for particle decomposition. I used: mpiexec mdrun -pd -deffnm nvt I obtain: apps/intel/ict/mpi/3.1.038/bin/mpdlib.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead from md5 import new as md5new NODEID=0 argc=4 :-) G R O M A C S (-: NODEID=2 argc=4 NODEID=6 argc=4 NODEID=1 argc=4 NODEID=5 argc=4 NODEID=11 argc=4 NODEID=3 argc=4 NODEID=7 argc=4 NODEID=8 argc=4 NODEID=9 argc=4 NODEID=10 argc=4 NODEID=4 argc=4 Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) starting mdrun 'Protein' 100 steps,500.0 ps. /apps/intel/ict/mpi/3.1.038/bin/mpdlib.py:27: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module. import sys, os, signal, popen2, socket, select, inspect /apps/intel/ict/mpi/3.1.038/bin/mpdlib.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead from md5 import new as md5new Then trajectory files are empty Your MPI configuration is probably broken. You should observe similar output from mdrun without using -pd. You should find out if a simple MPI test program can run. 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] mdrun -pd
On Wed, Feb 29, 2012 at 1:47 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/03/2012 12:31 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to use option -p of mdrun for particle decomposition. I used: mpiexec mdrun -pd -deffnm nvt I obtain: apps/intel/ict/mpi/3.1.038/**bin/mpdlib.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead from md5 import new as md5new NODEID=0 argc=4 :-) G R O M A C S (-: NODEID=2 argc=4 NODEID=6 argc=4 NODEID=1 argc=4 NODEID=5 argc=4 NODEID=11 argc=4 NODEID=3 argc=4 NODEID=7 argc=4 NODEID=8 argc=4 NODEID=9 argc=4 NODEID=10 argc=4 NODEID=4 argc=4 Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) starting mdrun 'Protein' 100 steps,500.0 ps. /apps/intel/ict/mpi/3.1.038/**bin/mpdlib.py:27: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module. import sys, os, signal, popen2, socket, select, inspect /apps/intel/ict/mpi/3.1.038/**bin/mpdlib.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead from md5 import new as md5new Then trajectory files are empty Your MPI configuration is probably broken. You should observe similar output from mdrun without using -pd. You should find out if a simple MPI test program can run. Well, without -pd everything works fine. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] using g_angle
Hi Mark, Thanks for your answer. What I'm trying to do is calculate the value in degrees of the angles listed in my index file. If my index file looks like [ dihedral 1 ] 2 7 9 10 [ dihedral 2 ] 10 16 18 19 then if I use the command line g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -ov angav_prova3.xvg -all -type dihedral or the same with the flag -od, what I get is an interactive menu where I have to choose the group and if I choose one then I obtain an output file which looks like # This file was created Wed Feb 29 14:54:55 2012 # by the following command: # /home/cocktail/vitalini/gromacs_special/bin/g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -od angav_prova3.xvg -all -type dihedral # # /home/cocktail/vitalini/gromacs_special/bin/g_angle is part of G R O M A C S: # # Great Red Oystrich Makes All Chemists Sane # @title Dihedral Distribution: dihedral @xaxis label Degrees @yaxis label @TYPE xy @subtitle average angle: -6192.3\So\N -1090.00 -1081.00 -1070.00 Which does what I'm looking for but this means that I'll need a file for each angle. Is there a faster way to get a file that has like two columns, one for the dihedral and another one for the angles? Thanks Francesca 2012/2/29 Mark Abraham mark.abra...@anu.edu.au: On 29/02/2012 11:54 PM, francesca vitalini wrote: 2012/2/29 Mark Abrahammark.abra...@anu.edu.au: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. Actually mk_angndx gies me the angles for phi and psi while instead I need omega and they are put in a strange format like in groups of 8 instead of 4. Whitespace inside the index group probably doesn't matter. However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is instead to know the value in degrees of each angle in the ndx file. Do you have any suggestions apart from building an index file for each angle? g_angle -ov -all with each angle in its own group. What do you mean with each angle in its own group? something like [dihedrals] 2 5 9 10 [dihedrals] 10 13 16 18 ... Yes, but with unique group names - but it turns out I was wrong to suggest that. Your index file above is fine. Isn't it equivalent to build differend index files? anyway the -ov flag gives the average over time, but I need the angles just at one time, that is why I was using -od but it just plots the distribution of all angles together. Any help? Which part of the output of g_angle -ov **-all** doesn't suit you? Mark Thanks Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using g_angle
On 1/03/2012 1:00 AM, francesca vitalini wrote: Hi Mark, Thanks for your answer. What I'm trying to do is calculate the value in degrees of the angles listed in my index file. If my index file looks like [ dihedral 1 ] 2 7 9 10 [ dihedral 2 ] 10 16 18 19 I said in my last email that my suggestion of a separate group group for each angle was wrong and that your original index file like [ dihedrals ] 2 5 9 10 10 15 18 19 . was fine. Please try that with g_angle -ov -all. I get output like # This file was created Mon Feb 20 12:32:15 2012 # by the following command: # g_angle -f 005_5 -type dihedral -all -ov 005_5_angles.xvg -n ../1oei_sim_backbone_angle.ndx # # g_angle is part of G R O M A C S: # # GRoups of Organic Molecules in ACtion for Science # @title Average Angle: Backbone_dihedral_angles @xaxis label Time (ps) @yaxis label Angle (degrees) @TYPE xy 245757.019.937 1.923 -61.394 -74.23627.453 -2.719 -179.19496.730 -27.46843.121-8.608-0.480 -0.764 0.001 -179.750 170.982 157.245 -174.93337.563 40.85493.32919.823 169.543 129.37140.443 -149.558 8.19843.427 100.08986.565 154.344 171.80452.401 -158.57127.166 -143.25339.944 6.985 178.488 179.865 -0.432 179.965 -179.957 179.499 -179.774 -179.788 107.176 151.312 -37.770 245762.022.309-1.821 -60.416 -73.830 -21.904 -2.231 -179.11196.693 -114.41440.600 -154.543 0.922 -2.143 0.932 179.704 -71.467 147.204 171.57152.328 39.06970.499 3.113 179.35591.08643.155 133.656 -22.50523.643 104.997 105.160 151.335 -176.456 176.378 23.691 6.447 -102.51243.83733.328 -179.572 -179.286 1.288 179.801 179.207 -179.029 -178.575 179.950 151.692 164.967-4.967 245763.036.760-1.567 -59.734 -74.259 -88.956 9.191 175.88091.328 -106.96238.466 -159.767-0.092 1.363-0.665 -179.743 -63.435 159.398 168.16742.926 40.20186.05815.792 171.260 108.56437.481 148.734 -19.16341.60395.716 100.927 159.081 177.076 170.625 18.81411.879 -108.60842.25131.301 -179.193 -179.047 0.401 -179.484 179.431 179.957 179.578 179.770 143.532 159.744-1.341 Mark then if I use the command line g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -ov angav_prova3.xvg -all -type dihedral or the same with the flag -od, what I get is an interactive menu where I have to choose the group and if I choose one then I obtain an output file which looks like # This file was created Wed Feb 29 14:54:55 2012 # by the following command: # /home/cocktail/vitalini/gromacs_special/bin/g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -od angav_prova3.xvg -all -type dihedral # # /home/cocktail/vitalini/gromacs_special/bin/g_angle is part of G R O M A C S: # # Great Red Oystrich Makes All Chemists Sane # @title Dihedral Distribution: dihedral @xaxis label Degrees @yaxis label @TYPE xy @subtitle average angle: -6192.3\So\N -1090.00 -1081.00 -1070.00 Which does what I'm looking for but this means that I'll need a file for each angle. Is there a faster way to get a file that has like two columns, one for the dihedral and another one for the angles? Thanks Francesca 2012/2/29 Mark Abrahammark.abra...@anu.edu.au: On 29/02/2012 11:54 PM, francesca vitalini wrote: 2012/2/29 Mark Abrahammark.abra...@anu.edu.au: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. Actually mk_angndx gies me the angles for phi and psi while instead I need omega and they are put in a strange format like in groups of 8 instead of 4. Whitespace inside the index group probably doesn't matter. However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is instead to know the value in degrees of each angle in the ndx file. Do you have any suggestions apart from building an index file for each angle? g_angle -ov -all with each angle in its own group. What do you mean with each angle in its own group? something like [dihedrals] 2 5 9 10 [dihedrals] 10 13 16 18 ... Yes, but with unique group names - but it turns out I was wrong to suggest that. Your index file above is fine. Isn't it equivalent to build differend index files? anyway the -ov flag gives the average over time, but I need the angles just at one time, that is why I was using -od but it just plots the distribution of all angles together. Any help? Which part of the output of g_angle -ov **-all** doesn't suit you? Mark Thanks
Re: [gmx-users] md in vacuo
On 29 February 2012 14:04, Mark Abraham mark.abra...@anu.edu.au wrote: On 29/02/2012 8:33 PM, Thomas Evangelidis wrote: Dear GROMACS community, I use the following parameters to run MD of ethane in vacuo. Then I calculate the H-C-C-H dihedral angle distribution and from that the rotational energy barrier using the formula DeltG=-k*T*ln(x), where x is the dihedral value. The rotational energy barrier is correct (~ 12 kJ) with all-bond constraints, but not with h-bond or no bond constraints. Could anyone tell me which other parameters to tweak in order to get the correct dihedral angle distribution without any bond constraints. Thanks in advance. Thomas integrator = md tinit= 0.0 dt = 0.002 This is too long if you are not using all-atom constraints. See manual 6.5 for discussion. Yes, I am sorry, I forgot to mention that in that case I use dt=0.001 and nsteps=500. Mark nsteps = 250 init_step= 0 simulation_part = 1 comm-mode= Angular nstcomm = 20 comm-grps= emtol= 0.01 emstep = 0.01 niter= 0 fcstep = 0 nstcgsteep = 1000 nbfgscorr= 10 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstcalcenergy= -1 nstenergy= 500 nstxtcout= 100 xtc-precision= 1000 xtc-grps = energygrps = System nstlist = 0 ns_type = simple pbc = no periodic_molecules = no rlist= 0 rlistlong= -1 coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 0.0 epsilon_r= 1.0 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 0 DispCorr = no table-extension = 1 energygrp_table = implicit_solvent = No tcoupl = v-rescale nsttcouple = 5 nh-chain-length = 10 tc-grps = System tau_t= 0.1 ref_t= 300 Pcoupl = no Pcoupltype = Isotropic nstpcouple = -1 tau_p= 1 compressibility = ref_p= 1.01.01.0 refcoord_scaling = No andersen_seed= 815131 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR= no shake-tol= 1e-04 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 morse= no -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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 -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] using g_angle
Thank you. It worked now. Best Francesca 2012/2/29 Mark Abraham mark.abra...@anu.edu.au: On 1/03/2012 1:00 AM, francesca vitalini wrote: Hi Mark, Thanks for your answer. What I'm trying to do is calculate the value in degrees of the angles listed in my index file. If my index file looks like [ dihedral 1 ] 2 7 9 10 [ dihedral 2 ] 10 16 18 19 I said in my last email that my suggestion of a separate group group for each angle was wrong and that your original index file like [ dihedrals ] 2 5 9 10 10 15 18 19 . was fine. Please try that with g_angle -ov -all. I get output like # This file was created Mon Feb 20 12:32:15 2012 # by the following command: # g_angle -f 005_5 -type dihedral -all -ov 005_5_angles.xvg -n ../1oei_sim_backbone_angle.ndx # # g_angle is part of G R O M A C S: # # GRoups of Organic Molecules in ACtion for Science # @ title Average Angle: Backbone_dihedral_angles @ xaxis label Time (ps) @ yaxis label Angle (degrees) @TYPE xy 245757.0 19.937 1.923 -61.394 -74.236 27.453 -2.719 -179.194 96.730 -27.468 43.121 -8.608 -0.480 -0.764 0.001 -179.750 170.982 157.245 -174.933 37.563 40.854 93.329 19.823 169.543 129.371 40.443 -149.558 8.198 43.427 100.089 86.565 154.344 171.804 52.401 -158.571 27.166 -143.253 39.944 6.985 178.488 179.865 -0.432 179.965 -179.957 179.499 -179.774 -179.788 107.176 151.312 -37.770 245762.0 22.309 -1.821 -60.416 -73.830 -21.904 -2.231 -179.111 96.693 -114.414 40.600 -154.543 0.922 -2.143 0.932 179.704 -71.467 147.204 171.571 52.328 39.069 70.499 3.113 179.355 91.086 43.155 133.656 -22.505 23.643 104.997 105.160 151.335 -176.456 176.378 23.691 6.447 -102.512 43.837 33.328 -179.572 -179.286 1.288 179.801 179.207 -179.029 -178.575 179.950 151.692 164.967 -4.967 245763.0 36.760 -1.567 -59.734 -74.259 -88.956 9.191 175.880 91.328 -106.962 38.466 -159.767 -0.092 1.363 -0.665 -179.743 -63.435 159.398 168.167 42.926 40.201 86.058 15.792 171.260 108.564 37.481 148.734 -19.163 41.603 95.716 100.927 159.081 177.076 170.625 18.814 11.879 -108.608 42.251 31.301 -179.193 -179.047 0.401 -179.484 179.431 179.957 179.578 179.770 143.532 159.744 -1.341 Mark then if I use the command line g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -ov angav_prova3.xvg -all -type dihedral or the same with the flag -od, what I get is an interactive menu where I have to choose the group and if I choose one then I obtain an output file which looks like # This file was created Wed Feb 29 14:54:55 2012 # by the following command: # /home/cocktail/vitalini/gromacs_special/bin/g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -od angav_prova3.xvg -all -type dihedral # # /home/cocktail/vitalini/gromacs_special/bin/g_angle is part of G R O M A C S: # # Great Red Oystrich Makes All Chemists Sane # @ title Dihedral Distribution: dihedral @ xaxis label Degrees @ yaxis label @TYPE xy @ subtitle average angle: -6192.3\So\N -109 0.00 -108 1.00 -107 0.00 Which does what I'm looking for but this means that I'll need a file for each angle. Is there a faster way to get a file that has like two columns, one for the dihedral and another one for the angles? Thanks Francesca 2012/2/29 Mark Abrahammark.abra...@anu.edu.au: On 29/02/2012 11:54 PM, francesca vitalini wrote: 2012/2/29 Mark Abrahammark.abra...@anu.edu.au: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. Actually mk_angndx gies me the angles for phi and psi while instead I need omega and they are put in a strange format like in groups of 8 instead of 4. Whitespace inside the index group probably doesn't matter. However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is instead to know the value in degrees of each angle in the ndx file. Do you have any suggestions apart from building an index file for each angle? g_angle -ov -all with each angle in its own group. What do you mean with each angle in its own group? something like [dihedrals] 2 5 9 10 [dihedrals] 10 13 16 18 ... Yes, but with unique group names - but it turns out I was wrong to suggest that. Your index file above is fine. Isn't it equivalent to build differend index files? anyway the -ov flag gives the average over time, but I need the angles just at one time, that is why I was using -od but it
Re: [gmx-users] PBC - Protein and Ligands
Steven Neumann wrote: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The problem I face is PBC which I cannot get rid of. I used: 1. First make your molecules whole if you want them whole (system). trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame (system) trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc So the trajecory of my ligands is smooth but they do do bind to the different periodic images. As i know it is impossible to obtain the proper trajectory of all of them I just want to obtain the realistic final positions of my system to extract pdb file for further umbrella sampling. Any suggestions? If you have a single protein to which all the molecules bind, you can simply: trjconv -s md298.tpr -f md298SKIP4.xtc -o center.xtc -center (center on protein, output system) trjconv -s md298.tpr -f center.xtc -o fit.xtc -fit rot+trans The protein will stay in the center of the box, with its rotational and translational motions fitted. It should produce a very smooth trajectory. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PBC - Protein and Ligands
On 1 Mar, 2012, at 1:01, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The problem I face is PBC which I cannot get rid of. I used: 1. First make your molecules whole if you want them whole (system). trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame (system) trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc So the trajecory of my ligands is smooth but they do do bind to the different periodic images. As i know it is impossible to obtain the proper trajectory of all of them I just want to obtain the realistic final positions of my system to extract pdb file for further umbrella sampling. Any suggestions? You may wanna try Trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -ur compact -o pdbs.pdb -dt 1000 Please change dt if necessary. Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PBC - Protein and Ligands
i always did it (successfully) with one single command: trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n ../../index.ndx regards vedat Am 29.02.2012 18:01, schrieb Steven Neumann: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The problem I face is PBC which I cannot get rid of. I used: 1.First make your molecules whole if you want them whole (system). trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc 2.Cluster your molecules/particles if you want them clustered 3.Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb 4.Remove jumps if you want to have them removed using the first frame (system) trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc So the trajecory of my ligands is smooth but they do do bind to the different periodic images. As i know it is impossible to obtain the proper trajectory of all of them I just want to obtain the realistic final positions of my system to extract pdb file for further umbrella sampling. Any suggestions? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Positive Coul. recip. term
The parameters I used are from the following reference: Canongia Lopes and Padua, J. Phys. Chem. B 2004, 108, 16893 This paper gives the bonded parameters of the anion and the non-bonded parameters of both ions. The bonded parameters of the cation were obtained (as indicated in the reference above) from the OPLS force field. (Rizzo and Jorgensen, JACS 1999, 121, 4827). Fixing the dihedral error I mentioned in my last email has kept the system from crashing. The coul. recip term is still positive, however. g_pme_error gave a Direct space error estimate of 9.8e-3 kJ/mol*nm and a Reciprocal space error estimate of 3.3 kJ/mol*nm. On Wed, Feb 29, 2012 at 3:47 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote: The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and the force field is from Lopes (CLaP). I tried deleting all of the cation dihedrals from the itp file and found that the run did not crash, although it still had a positive coul recip term. Upon examination of the cation dihedrals I noticed that there was a typo in which a set of unbonded carbons were put together in a dihedral term. Perhaps this is what made the previous runs crash. Even with this correction, the coul. recip. term is still positive. I have tried smaller time steps and changing ewald_tol to 1e-3, but these have not resolved this issue. How can I calculate the error in the electrostatic force? Denny The error of PME can be estimated a priori with the tool g_pme_error. I would suggest to tune it to a bound below 1e-3. I took a look at the force field parameters for the pyrrolidinium, which is published by Lopes in 2006, and I assume you use this parameters, are you ? I do not understand Table I in this paper. The dihedral parameters are just given for V_2 and V_4, and for a certain dihedral they are even set to zero. If you use this force field, how are the other parameters obtained ? Are they zero or do they correspond to the OPLS values given in the reference cited on the top of the table ? /Flo On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote: Thank you both for your replies. I currently have another ionic liquid running just fine on the same gromacs build (compiled the tpr file yesterday), so I am reluctant to conclude that the problem is with the linking. Please let me know if you disagree. The force field I am using was published in 2004 and has been validated by another group. I have double and triple checked my itp files to make sure they match the force field, but it's possible there are still some errors there. Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who validated it, I am just curious, and what is the ionic liquid ? Though you are constraining the hbonds, I would be cautious with the time step of 2fs, because it might be, that the eigenfrequency of the anionic bonds requires a shorter time step, but this should not be the problem of a positive Coulomb energy. Have you calculated the error in the electrostatic force ? I would suggest to tune it to a limit of 1e-3, perhaps this resolves the problem of the positive Coulomb term. Perhaps some 1--4 and dihedral interactions are missing in the itp file, so assure if all of them are provided correctly. /Flo I agree that this is very strange and feel that there must be something fundamentally wrong in the mdp file or deeper. I have included my mdp file below. title = PMP+TFN cpp = /lib/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 1000 ; total 20 ns nstcomm = 10 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = Cut-off rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol
Re: [gmx-users] Positive Coul. recip. term
On Wed, 2012-02-29 at 11:12 -0700, Denny Frost wrote: The parameters I used are from the following reference: Canongia Lopes and Padua, J. Phys. Chem. B 2004, 108, 16893 This paper gives the bonded parameters of the anion and the non-bonded parameters of both ions. The bonded parameters of the cation were obtained (as indicated in the reference above) from the OPLS force field. (Rizzo and Jorgensen, JACS 1999, 121, 4827). Fixing the dihedral error I mentioned in my last email has kept the system from crashing. The coul. recip term is still positive, however. g_pme_error gave a Direct space error estimate of 9.8e-3 kJ/mol*nm and a Reciprocal space error estimate of 3.3 kJ/mol*nm. Look there is a big discrepancy between the real and reciprocal space error, such that your overall force has an error in the order of 10^0, but if you distribute the error over the real and reciprocal part by a change of ewald_rtol, you can descrease this error. g_pme_error with the flag -tune does this for you. Accordingly, by a decrease of the fourier spacing, the error can be further decreased to the desired accuracy. Hence you can check if the positive Coulomb term is an artefact of low accuracy. /Flo On Wed, Feb 29, 2012 at 3:47 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote: The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and the force field is from Lopes (CLaP). I tried deleting all of the cation dihedrals from the itp file and found that the run did not crash, although it still had a positive coul recip term. Upon examination of the cation dihedrals I noticed that there was a typo in which a set of unbonded carbons were put together in a dihedral term. Perhaps this is what made the previous runs crash. Even with this correction, the coul. recip. term is still positive. I have tried smaller time steps and changing ewald_tol to 1e-3, but these have not resolved this issue. How can I calculate the error in the electrostatic force? Denny The error of PME can be estimated a priori with the tool g_pme_error. I would suggest to tune it to a bound below 1e-3. I took a look at the force field parameters for the pyrrolidinium, which is published by Lopes in 2006, and I assume you use this parameters, are you ? I do not understand Table I in this paper. The dihedral parameters are just given for V_2 and V_4, and for a certain dihedral they are even set to zero. If you use this force field, how are the other parameters obtained ? Are they zero or do they correspond to the OPLS values given in the reference cited on the top of the table ? /Flo On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote: Thank you both for your replies. I currently have another ionic liquid running just fine on the same gromacs build (compiled the tpr file yesterday), so I am reluctant to conclude that the problem is with the linking. Please let me know if you disagree. The force field I am using was published in 2004 and has been validated by another group. I have double and triple checked my itp files to make sure they match the force field, but it's possible there are still some errors there. Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who validated it, I am just curious, and what is the ionic liquid ? Though you are constraining the hbonds, I would be cautious with the time step of 2fs, because it might be, that the eigenfrequency of the anionic bonds requires a shorter time step, but this should not be the problem of a positive Coulomb energy. Have you calculated the error in the electrostatic force ? I would suggest to tune it to a limit of 1e-3, perhaps this
RE: [gmx-users] quick question about restart
I use the second option there on all my simulations, using a script. Simulations are done in 10ns blocks, at the completion of that the pbs script submits the next job. Have found this way much less hassle, better computer utilisation etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Anna Marabotti Sent: Wednesday, 29 February 2012 9:48 PM To: gmx-users@gromacs.org Subject: [gmx-users] quick question about restart Dear gmx-users, I'm running my simulations on a machine with a queue system that stops the runs longer than 24 hours. Often, for my simulations, I need a longer time to complete the runs. Let's have an example. I have to run a 100ns-long simulation on a machine that produces 10ns/days simulation. I have two possibilities: First approach: I'm setting within the .mdp file a global duration of 100 ns. Then: grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, I see that the run has been stopped after 10 ns. I have the output_fullMD.cpt file. Then, I do: mdrun -s input_fullMD.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the run has been completed (then I will concatenate the .xtc, .edr, .trr files) Second approach: I'm setting within the .mdp file a global duration of 10 ns. Then (as above): grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, the run has been finished. Then, I continue the run for other 10 ns with: tpbconv -s input_fullMD.tpr -extend 1 -o input_fullMD_2.tpr mdrun -s input_fullMD_2.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the 100-ns run has been completed. Are the two procedure producing EXACTLY the same results, or not? Which is the best preferred procedure? Thank you very much Anna Anna Marabotti, Ph.D. Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man (Roberto Benigni, about Roberto Saviano) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to use charmm ff in gmx and carbohydrate forcefield
Dear Gromacs User and developers: Please help with 2 questions: 1) Does the converted charmm forcefield (charmm36 or 27) in gromacs include forcefield parameters for carbohydrate (sugar)? I looked through *itp and can not find them in converted charmm36 and 27 in gromacs. 2) How to convert charmm forcefield parameters and use in gromacs? To save time to look through gromacs source code, any expert can give some guidances? My question is beside the difference in the unit, like kcal, A (charmm) vs. kj, nm (gromacs), do i need to care about any conversion of the potential format? For example: i have a set of nonbonded and bonded parameters with the original charmm formate and want to use in gromacs, do i need to convert anything, because of the format difference in the potential formula, such as potential of vdw, bond, angle, dihedral angle, and improper dihedral angle before i add them to *itp and *rtp file? Thanks a lot for the information! Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to use charmm ff in gmx and carbohydrate forcefield
On 2012-02-29 05:11:48PM -0600, Tom wrote: Dear Gromacs User and developers: Please help with 2 questions: 1) Does the converted charmm forcefield (charmm36 or 27) in gromacs include forcefield parameters for carbohydrate (sugar)? I looked through *itp and can not find them in converted charmm36 and 27 in gromacs. The only sugars that ship with the conversions are the ribose variants found in dna and rna. You can extract those and rebalance the charges, but if you want something more exotic then you'll probably have to do the conversions from charmm36/xx 2) How to convert charmm forcefield parameters and use in gromacs? To save time to look through gromacs source code, any expert can give some guidances? My question is beside the difference in the unit, like kcal, A (charmm) vs. kj, nm (gromacs), do i need to care about any conversion of the potential format? For example: i have a set of nonbonded and bonded parameters with the original charmm formate and want to use in gromacs, do i need to convert anything, because of the format difference in the potential formula, such as potential of vdw, bond, angle, dihedral angle, and improper dihedral angle before i add them to *itp and *rtp file? Thanks a lot for the information! See: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060108.html which is codified in the tables of https://uab.hyperfine.info/trac/molsim/wiki/gromacs Charmm FF Conversion information. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing 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] on the dissociation of protein complex during MD
Dear All, Some of the complexes of PDB files in RCSB are not from protein-protein interaction, but from the packing of protein crystal. Thus in solution the protien complex may dissociate. However as for the protein are usually very large, and I regard it is difficult to observe that 2 (or more) subunit protein complex dissociate completely during MD simulation. Can you please introduce to me your experience that the protein complex sifnificantly dissociate during MD? I am looking forward to getting your reply. Cheers, Dialing-- 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] on the dissociation of protein complex during MD
On 1/03/2012 11:57 AM, Dialing Pretty wrote: Dear All, Some of the complexes of PDB files in RCSB are not from protein-protein interaction, but from the packing of protein crystal. Thus in solution the protien complex may dissociate. However as for the protein are usually very large, and I regard it is difficult to observe that 2 (or more) subunit protein complex dissociate completely during MD simulation. Can you please introduce to me your experience that the protein complex sifnificantly dissociate during MD? That's a very expensive way to observe whether the complex is thought to be real or not - if it is possible to get a reliable result. Reading the literature that led to the PDB contribution and about the protein generally will be much more productive. 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] dihedral distributions
Hi all, Can anyone guide me how one can obtain dihedral distributions of a polymer chain and how this can be used to ensure the equilibration of system? g_angle takes a list of dihedrals and provides the dihedral distribution of a given dihedral in the time interval -b to -e ? -- Thanks, J. -- 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] crashed run...
Hi GROMACS specialist, My MD run get crashed because of less memory. I given the command mdrun -s prev.tpr -f prev.trr -e prev.edr -o prev.trr -g prev.log -cpi -append -v Now is my system is started from the initial time or from the time of crash?? What is the process for to start from crash point??? My system showing much time for complete than before the crash... Thank you in advance.. Have a nice day.. -- 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] crashed run...
On 1/03/2012 5:30 PM, rama david wrote: Hi GROMACS specialist, My MD run get crashed because of less memory. I given the command mdrun -s prev.tpr -f prev.trr -e prev.edr -o prev.trr -g prev.log -cpi -append -v Now is my system is started from the initial time or from the time of crash?? It starts from the point contained in the .cpi file. What is the process for to start from crash point??? You can only restart from the point in the .cpi file, which will be some time before the crash. My system showing much time for complete than before the crash... Look in the log file and/or stdout and you'll probably have been told what's going on. 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] dihedral distributions
On 1/03/2012 5:07 PM, Juliette N. wrote: Hi all, Can anyone guide me how one can obtain dihedral distributions of a polymer chain and how this can be used to ensure the equilibration of system? g_angle takes a list of dihedrals and provides the dihedral distribution of a given dihedral in the time interval -b to -e ? Have a read of g_angle -h and try things out. You'll need to look in the literature for info on the kind of information you're looking for. 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
