[gmx-users] how to include Fe-S topology in .rtp file
hi all... I am simulating a protein with Fe-S cluster. What is the protocol for generating a .rtp file with Fe-S topology...As i am using ffG43a1 forcefield.. i searched FFG43a1bon.itp file for Fe-S bond, angle and dihedral type... but it is not there..what i should do?.. If anyone have the idea of the procedure..please outline me the procedure.. Thanks.. Amrita Ph.D scholar, Burdwan University. Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Nonrepeatable results for gromacs 4.0.5
Hi, For the record there is also the -reprod (reproducibility) that also turns off the dynamic FFTW plan optimization. With these options enabled you will lose a bit of performance, but should get binary identical runs even in parallel (as long as you use the same number of CPUs). Cheers, Erik On Jun 7, 2009, at 9:20 AM, David van der Spoel wrote: Jim Kress wrote: I've been doing multiple runs using gromacs v 4.0.5 mdrun and a constant topol.tpr input file. Unfortunately, the results that I get in my md.log differ from run to run. This is due to dynamic load balancing. Due to fluctuations in the CPU usage (e.g. due to operating system) your load will vary on each CPU and gromacs will try to balance it. Hence you get numerical differences because in a computer (a+b)+c != a+(b+c), and ultimately the trajectories will diverge. If you turn off dlb this should not happen. Please try it and report if you see the same effect without. For example, Run 1 Started mdrun on node 0 Fri May 22 22:53:51 2009 Step Time Lambda 00.00.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.95406e+021.04746e+024.97704e+014.13260e+01 1.40158e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.60139e+03 -2.64656e+04 -2.20714e+044.03780e+03 -1.80336e+04 Temperature Pressure (bar) Cons. rmsd () 3.03142e+02 -8.46977e+021.92470e-05 DD step 9 load imb.: force 29.9% At step 10 the performance loss due to force load imbalance is 8.6 % NOTE: Turning on dynamic load balancing DD step 99 vol min/aver 0.731 load imb.: force 6.9% Step Time Lambda 1000.20.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.05310e+021.30129e+025.63474e+011.81814e+01 1.44270e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.69491e+03 -2.69624e+04 -2.24148e+044.19456e+03 -1.82203e+04 Temperature Pressure (bar) Cons. rmsd () 3.14910e+02 -5.19031e+021.76248e-05 DD load balancing is limited by minimum cell size in dimension Y DD step 199 vol min/aver 0.766! load imb.: force 10.7% Step Time Lambda 2000.40.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.20550e+021.09068e+026.93319e+015.32511e+01 1.43458e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.78241e+03 -2.70319e+04 -2.23627e+044.13455e+03 -1.82281e+04 Temperature Pressure (bar) Cons. rmsd () 3.10405e+02 -5.01205e+021.70105e-05 DD load balancing is limited by minimum cell size in dimension Y DD step 299 vol min/aver 0.750! load imb.: force 3.3% Step Time Lambda 3000.60.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.17474e+028.65489e+015.24995e+014.72592e+01 1.44419e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 3.17643e+03 -2.72841e+04 -2.22597e+043.95024e+03 -1.83095e+04 Temperature Pressure (bar) Cons. rmsd () 2.96568e+021.40098e+031.55861e-05 DD step 399 vol min/aver 0.700 load imb.: force 5.9% Step Time Lambda 4000.80.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.43143e+029.93116e+017.16796e+014.63666e+01 1.46722e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.84150e+03 -2.70065e+04 -2.22372e+044.05976e+03 -1.81775e+04 Temperature Pressure (bar) Cons. rmsd () 3.04791e+022.48551e+021.61141e-05 DD step 499 vol min/aver 0.678 load imb.: force 6.6% Step Time Lambda 5001.00.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.19638e+028.98359e+018.99946e+015.16612e+01 1.46338e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.80267e+03 -2.68507e+04 -2.21335e+044.14195e+03 -1.79916e+04 Temperature Pressure (bar) Cons. rmsd () 3.10961e+02 -1.17210e+021.71420e-05 DD step 599 vol min/aver 0.678 load imb.: force 6.7% Step Time Lambda 6001.20.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.32938e+021.04322e+027.11343e+012.16046e+01 1.45770e+03 LJ (SR)
[gmx-users] problem in running grompp
hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows ''Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 843 Fatal error: Atomtype CA not found'' but is not CA the main chain alpha carbon...why is not grompp taking CA then? i can't make out where the problem lies? i little help on this shall be very encouraging. Thank You Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PME nodes
On Jun 6, 2009, at 1:20 PM, XAvier Periole wrote: On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote: XAvier Periole wrote: Dears, I am having troubles finding the better balance between the PME CPUs and the rest. I played with the rdd, rcon and -npme options but nothing really appears very straightforwardly best. I'd appreciate if some of you could post their experience in that matter. I mean the number of pme nodes as compared the total number of CPUs used. I think this info as been discussed recently on the list but the archive is not accessible. It may matter that I have a system containing about 7 atoms, a protein in a bilayer. Some advice that I got from Berk long ago has worked beautifully for me. You want a 3:1 PP:PME balance for a regular triclinic cell (grompp will report the relative PME load as 25% if your parameters create such a balance), 2:1 for an octahedron. My scaling has been great using this information, without having to alter -rdd, -rcon, etc. Thanks for the info. I got more or less to that ratio. Although a 2:1 PP:PME sometimes is better. However my problem now is to get 256 CPUs more efficient (ns/day) than 128 CPUs. The communications become a limiting factor ... can't get it to go faster! The system might be small, but not sure. I'll take a look at the CVS tool. There is also a version for gromacs 4.0.x available for download at www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ Regards, Carsten -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PME nodes
Hello, How can I compile the g_tune_pme program available at: http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ Many thanks, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in running grompp
Samik Bhattacharya wrote: hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows ''Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 843 Fatal error: Atomtype CA not found'' but is not CA the main chain alpha carbon...why is not grompp taking CA then? i can't make out where the problem lies? i little help on this shall be very encouraging. If you're seeing this error, then you've done something wrong when combining lipid.itp with the Gromos force field file. -Justin Thank You Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to include Fe-S topology in .rtp file
amri ta wrote: hi all... I am simulating a protein with Fe-S cluster. What is the protocol for generating a .rtp file with Fe-S topology...As i am using ffG43a1 forcefield.. i searched FFG43a1bon.itp file for Fe-S bond, angle and dihedral type... but it is not there..what i should do?.. If anyone have the idea of the procedure..please outline me the procedure.. Then the exceptionally difficult task of parameterization falls to you. Running a simulation with an Fe-S cluster will require very advanced knowledge of Gromacs and the force field for which you are designing the parameters. Take special note of the information here: http://oldwiki.gromacs.org/index.php/Exotic_Species -Justin Thanks.. Amrita Ph.D scholar, Burdwan University. Cricket on your mind? Visit the ultimate cricket website. Enter now! http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PME nodes
Hi, it's written at the begin of the .c file: * You can compile this tool using the Gromacs Makefile from the * share/gromacs/template directory, just replace 'template' by 'g_tune_pme' * where needed. To enable shell completions for g_tune_pme, just * copy the provided completion.* files to your Gromacs bin directory. Carsten On Jun 8, 2009, at 12:48 PM, Andrei Neamtu wrote: Hello, How can I compile the g_tune_pme program available at: http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ Many thanks, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Nonrepeatable results for gromacs 4.0.5
If you turn off dlb this should not happen. Please try it and report if you see the same effect without. No, I do not see the same effect if I turn off dlb. However, I am concerned that the magnitude of the differences between runs exceeds the expected, normal variability (as defined by the RMS deviations of each run), so I am exploring that. Also, if I turn on nosum, as suggested by mdrun, the run with dlb turned on diverges. This is also a cause for concern. Jim -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Sunday, June 07, 2009 3:20 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Nonrepeatable results for gromacs 4.0.5 Jim Kress wrote: I've been doing multiple runs using gromacs v 4.0.5 mdrun and a constant topol.tpr input file. Unfortunately, the results that I get in my md.log differ from run to run. This is due to dynamic load balancing. Due to fluctuations in the CPU usage (e.g. due to operating system) your load will vary on each CPU and gromacs will try to balance it. Hence you get numerical differences because in a computer (a+b)+c != a+(b+c), and ultimately the trajectories will diverge. If you turn off dlb this should not happen. Please try it and report if you see the same effect without. For example, Run 1 Started mdrun on node 0 Fri May 22 22:53:51 2009 Step Time Lambda 00.00.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.95406e+021.04746e+024.97704e+014.13260e+01 1.40158e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.60139e+03 -2.64656e+04 -2.20714e+044.03780e+03 -1.80336e+04 Temperature Pressure (bar) Cons. rmsd () 3.03142e+02 -8.46977e+021.92470e-05 DD step 9 load imb.: force 29.9% At step 10 the performance loss due to force load imbalance is 8.6 % NOTE: Turning on dynamic load balancing DD step 99 vol min/aver 0.731 load imb.: force 6.9% Step Time Lambda 1000.20.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.05310e+021.30129e+025.63474e+011.81814e+01 1.44270e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.69491e+03 -2.69624e+04 -2.24148e+044.19456e+03 -1.82203e+04 Temperature Pressure (bar) Cons. rmsd () 3.14910e+02 -5.19031e+021.76248e-05 DD load balancing is limited by minimum cell size in dimension Y DD step 199 vol min/aver 0.766! load imb.: force 10.7% Step Time Lambda 2000.40.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.20550e+021.09068e+026.93319e+015.32511e+01 1.43458e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.78241e+03 -2.70319e+04 -2.23627e+044.13455e+03 -1.82281e+04 Temperature Pressure (bar) Cons. rmsd () 3.10405e+02 -5.01205e+021.70105e-05 DD load balancing is limited by minimum cell size in dimension Y DD step 299 vol min/aver 0.750! load imb.: force 3.3% Step Time Lambda 3000.60.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.17474e+028.65489e+015.24995e+014.72592e+01 1.44419e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 3.17643e+03 -2.72841e+04 -2.22597e+043.95024e+03 -1.83095e+04 Temperature Pressure (bar) Cons. rmsd () 2.96568e+021.40098e+031.55861e-05 DD step 399 vol min/aver 0.700 load imb.: force 5.9% Step Time Lambda 4000.80.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.43143e+029.93116e+017.16796e+014.63666e+01 1.46722e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.84150e+03 -2.70065e+04 -2.22372e+044.05976e+03 -1.81775e+04 Temperature Pressure (bar) Cons. rmsd () 3.04791e+022.48551e+021.61141e-05 DD step 499 vol min/aver 0.678 load imb.: force 6.6% Step Time Lambda 5001.00.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.19638e+028.98359e+018.99946e+015.16612e+01 1.46338e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.80267e+03 -2.68507e+04 -2.21335e+044.14195e+03
Re: [gmx-users] Nonrepeatable results for gromacs 4.0.5
jimkress_58 skrev: If you turn off dlb this should not happen. Please try it and report if you see the same effect without. No, I do not see the same effect if I turn off dlb. However, I am concerned that the magnitude of the differences between runs exceeds the expected, normal variability (as defined by the RMS deviations of each run), so I am exploring that. Also, if I turn on nosum, as suggested by mdrun, the run with dlb turned on diverges. This is also a cause for concern. No, that's expected. See David's reply below. Nosum is only good for reducing communication, thus increasing performance. /Erik Jim -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Sunday, June 07, 2009 3:20 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Nonrepeatable results for gromacs 4.0.5 Jim Kress wrote: I've been doing multiple runs using gromacs v 4.0.5 mdrun and a constant topol.tpr input file. Unfortunately, the results that I get in my md.log differ from run to run. This is due to dynamic load balancing. Due to fluctuations in the CPU usage (e.g. due to operating system) your load will vary on each CPU and gromacs will try to balance it. Hence you get numerical differences because in a computer (a+b)+c != a+(b+c), and ultimately the trajectories will diverge. If you turn off dlb this should not happen. Please try it and report if you see the same effect without. For example, Run 1 Started mdrun on node 0 Fri May 22 22:53:51 2009 Step Time Lambda 00.00.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.95406e+021.04746e+024.97704e+014.13260e+01 1.40158e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.60139e+03 -2.64656e+04 -2.20714e+044.03780e+03 -1.80336e+04 Temperature Pressure (bar) Cons. rmsd () 3.03142e+02 -8.46977e+021.92470e-05 DD step 9 load imb.: force 29.9% At step 10 the performance loss due to force load imbalance is 8.6 % NOTE: Turning on dynamic load balancing DD step 99 vol min/aver 0.731 load imb.: force 6.9% Step Time Lambda 1000.20.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.05310e+021.30129e+025.63474e+011.81814e+01 1.44270e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.69491e+03 -2.69624e+04 -2.24148e+044.19456e+03 -1.82203e+04 Temperature Pressure (bar) Cons. rmsd () 3.14910e+02 -5.19031e+021.76248e-05 DD load balancing is limited by minimum cell size in dimension Y DD step 199 vol min/aver 0.766! load imb.: force 10.7% Step Time Lambda 2000.40.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.20550e+021.09068e+026.93319e+015.32511e+01 1.43458e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.78241e+03 -2.70319e+04 -2.23627e+044.13455e+03 -1.82281e+04 Temperature Pressure (bar) Cons. rmsd () 3.10405e+02 -5.01205e+021.70105e-05 DD load balancing is limited by minimum cell size in dimension Y DD step 299 vol min/aver 0.750! load imb.: force 3.3% Step Time Lambda 3000.60.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.17474e+028.65489e+015.24995e+014.72592e+01 1.44419e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 3.17643e+03 -2.72841e+04 -2.22597e+043.95024e+03 -1.83095e+04 Temperature Pressure (bar) Cons. rmsd () 2.96568e+021.40098e+031.55861e-05 DD step 399 vol min/aver 0.700 load imb.: force 5.9% Step Time Lambda 4000.80.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.43143e+029.93116e+017.16796e+014.63666e+01 1.46722e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 2.84150e+03 -2.70065e+04 -2.22372e+044.05976e+03 -1.81775e+04 Temperature Pressure (bar) Cons. rmsd () 3.04791e+022.48551e+021.61141e-05 DD step 499 vol min/aver 0.678 load imb.: force 6.6% Step Time Lambda 5001.00.0 Energies (kJ/mol)
Re: [gmx-users] about epsion_surface
lammps lammps wrote: Dear, I do not know where should I have to use the epsion_surface? The system include a CG membrane, a charged macromolecule above the membrane and some counterions ? It is suitable to using this parameter epsilon_surface = 1? It is appricated if some one tell me something about how to use this parameter. Thanks in advance. The manual seems to describe its function fairly well. See section 7.3. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs on glacier
Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites Charge group distribution at step 0: 101 147 137 152 Grid: 5 x 3 x 3 cells in the output file reported by cluster: pwd= /home/ppirzade/GROMACS/mytests/small-box-of-water Got 4 slots. compute-1-34 compute-1-34 compute-2-20 compute-2-20 Starting run at: Mon Jun 8 10:27:52 MDT 2009 p2_22627: p4_error: Timeout in establishing connection to remote process: 0 rm_l_2_22748: (301.332031) net_send: could not write to fd=5, errno = 32 p2_22627: (301.332031) net_send: could not write to fd=5, errno = 32 p0_21851: (302.351562) net_recv failed for fd = 6 p0_21851: p4_error: net_recv read, errno = : 104 p0_21851: (306.359375) net_send: could not write to fd=4, errno = 32 Ending run at: Mon Jun 8 10:32:59 MDT 2009 in the error file reported by cluster: Reading file npttest.tpr, VERSION 4.0.4 (single precision) Making 1D domain decomposition 4 x 1 x 1 Killed by signal 2.^M Killed by signal 2.^M Killed by signal 2.^M To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Energies in simulation
Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am currently using. I double-checked the parameters I gave in the .itp with TIP4P and TIP5P to make sure everything is correct in format and unit. But I can not figure out the problem. Any ideas? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote: Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am currently using. I double-checked the parameters I gave in the .itp with TIP4P and TIP5P to make sure everything is correct in format and unit. But I can not figure out the problem. Any ideas? Is there any self-energy involved (i.e. a monomer energy that yo have to subtract)? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energies in simulation
To the best of my knowledge no, but how can I check that? -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: June 8, 2009 11:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energies in simulation Payman Pirzadeh wrote: Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am currently using. I double-checked the parameters I gave in the .itp with TIP4P and TIP5P to make sure everything is correct in format and unit. But I can not figure out the problem. Any ideas? Is there any self-energy involved (i.e. a monomer energy that yo have to subtract)? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote: To the best of my knowledge no, but how can I check that? A. read the original paper: is your topology correct? Are the simulation parameters the same? B. post the itp file here and mdp file and specify energy and expected energy. How about energy units? -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: June 8, 2009 11:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energies in simulation Payman Pirzadeh wrote: Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am currently using. I double-checked the parameters I gave in the .itp with TIP4P and TIP5P to make sure everything is correct in format and unit. But I can not figure out the problem. Any ideas? Is there any self-energy involved (i.e. a monomer energy that yo have to subtract)? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, … it will crash. Following are the last lines reported in different files: “In the log file of the code”: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energies in simulation
Here is the content of .itp file which I developed:
; This is an itp file to describe water's six-site model by H. Nada and J.P.
J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites and
3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is 111.00
degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name masscharge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.000.00
LW 0.00-0.044 D 0.000.00
[ moleculetype ]
;molnamenrexcl
SOL 1
[ atoms ]
; nratomtyperesnr residuename atomcgnrcharge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OWfunctiondoh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} = Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function 1
;
; site fromfunctiona b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} = Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH bonds,
a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} = The denominator is the
magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site fromfunctiona b c
5 1 2 3 4 -0.437172388-0.437172388
8.022961206
6 1 2 3 4 -0.437172388-0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
And here is the mdp file which I used for the simulation run:
cpp = cpp
include = -I../top
define =
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 100 ;10 ns
comm_mode= linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy= 5000
nstxtcout= 1000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist= 0.9
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
epsilon_r= 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft= yes
; Temperature coupling
tcoupl = Berendsen
tc-grps = System
tau_t= 0.1
ref_t= 300
; Pressure Coupling
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p= 1.0
compressibility = 5.5e-5
ref_p= 1.0
gen_vel = yes
The expected Potential energy is supposed to be around -41.5kJ/mol while my
potential is around -22.2kJ/mol. I calculated the energies by g_energy
command.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:13 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
To the best of my knowledge no, but how can I check that?
A. read the original paper: is your topology correct? Are the simulation
parameters the same?
B. post the itp file here and mdp file and specify energy and expected
energy. How about energy units?
-Original Message-
From: gmx-users-boun...@gromacs.org
Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Here is the content of .itp file which I developed:
; This is an itp file to describe water's six-site model by H. Nada and J.P.
J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites and
3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is 111.00
degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name masscharge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.000.00
LW 0.00-0.044 D 0.000.00
[ moleculetype ]
;molnamenrexcl
SOL 1
[ atoms ]
; nratomtyperesnr residuename atomcgnrcharge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OWfunctiondoh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} = Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function 1
;
; site fromfunctiona b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} = Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH bonds,
a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} = The denominator is the
magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site fromfunctiona b c
5 1 2 3 4 -0.437172388-0.437172388
8.022961206
6 1 2 3 4 -0.437172388-0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
And here is the mdp file which I used for the simulation run:
cpp = cpp
include = -I../top
define =
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 100 ;10 ns
comm_mode= linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy= 5000
nstxtcout= 1000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist= 0.9
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
epsilon_r= 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft= yes
; Temperature coupling
tcoupl = Berendsen
tc-grps = System
tau_t= 0.1
ref_t= 300
; Pressure Coupling
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p= 1.0
compressibility = 5.5e-5
ref_p= 1.0
gen_vel = yes
The expected Potential energy is supposed to be around -41.5kJ/mol while my
potential is around -22.2kJ/mol. I calculated the energies by g_energy
command.
And do yo have the right density?
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:13 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
To the best of my knowledge no, but how can I check that?
A. read the original paper: is your topology correct? Are the simulation
parameters the same?
B. post the itp file here and mdp file and specify energy and expected
energy. How about energy units?
RE: [gmx-users] gromacs on glacier
Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energies in simulation
Well, when I set the box, I used 'editconf' command to rescale the box to
have the right density which was ~997. After simulation, I got the
following:
Energy Average RMSD Fluct. Drift
Tot-Drift
---
Density (SI)956.765150.266130.596 0.257477
257.477
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Here is the content of .itp file which I developed:
; This is an itp file to describe water's six-site model by H. Nada and
J.P.
J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and
3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00
degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name masscharge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.000.00
LW 0.00-0.044 D 0.000.00
[ moleculetype ]
;molnamenrexcl
SOL 1
[ atoms ]
; nratomtyperesnr residuename atomcgnrcharge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OWfunctiondoh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} = Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function 1
;
; site fromfunctiona b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j))
+
b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} = Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds,
a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} = The denominator is
the
magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site fromfunctiona b c
5 1 2 3 4 -0.437172388-0.437172388
8.022961206
6 1 2 3 4 -0.437172388-0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
And here is the mdp file which I used for the simulation run:
cpp = cpp
include = -I../top
define =
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 100 ;10 ns
comm_mode= linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy= 5000
nstxtcout= 1000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist= 0.9
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
epsilon_r= 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft= yes
; Temperature coupling
tcoupl = Berendsen
tc-grps = System
tau_t= 0.1
ref_t= 300
; Pressure Coupling
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p= 1.0
compressibility = 5.5e-5
ref_p= 1.0
gen_vel
Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote: Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. This is pretty much the standard installation procedure. What we also need to know are the compilers used, etc. for the installation. The error you're getting is from MPICH. Which version is installed on the cluster? It may be old and buggy. In any case, you can try to install something newer, like a recent version of OpenMPI (which we have on our cluster); it may be more reliable. Only a random thought, means nothing unless we know what you have installed :) What about the contents of your system, as I asked before? Do you really have a 100% virtual site system? -Justin Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Well, when I set the box, I used 'editconf' command to rescale the box to
have the right density which was ~997. After simulation, I got the
following:
Energy Average RMSD Fluct. Drift
Tot-Drift
---
Density (SI)956.765150.266130.596 0.257477
257.477
The RMSD is very large. Are you sure this is in equilibrium? It could be
that your box is exploding. Please check as well that the strange twin
range cut-off that you are using is what the original authors used.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Here is the content of .itp file which I developed:
; This is an itp file to describe water's six-site model by H. Nada and
J.P.
J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and
3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00
degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name masscharge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.000.00
LW 0.00-0.044 D 0.000.00
[ moleculetype ]
;molnamenrexcl
SOL 1
[ atoms ]
; nratomtyperesnr residuename atomcgnrcharge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OWfunctiondoh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} = Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function 1
;
; site fromfunctiona b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j))
+
b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} = Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds,
a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} = The denominator is
the
magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site fromfunctiona b c
5 1 2 3 4 -0.437172388-0.437172388
8.022961206
6 1 2 3 4 -0.437172388-0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
And here is the mdp file which I used for the simulation run:
cpp = cpp
include = -I../top
define =
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 100 ;10 ns
comm_mode= linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy= 5000
nstxtcout= 1000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist= 0.9
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
epsilon_r= 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft= yes
; Temperature coupling
tcoupl = Berendsen
tc-grps = System
tau_t= 0.1
ref_t= 300
; Pressure Coupling
Pcoupl =
RE: [gmx-users] gromacs on glacier
Dear Justin, Here is the mpich version: MPICH Version: 1.2.7p1 MPICH Release date: $Date: 2005/11/04 11:54:51$ MPICH Patches applied: none MPICH configure:-prefix=/share/apps/intel/mpich/ MPICH Device: ch_p4 Also the gcc compiler: gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9) Copyright (C) 2006 Free Software Foundation, Inc. About the system, I have water model with 3 atom sites and 3 virtual sites. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:56 AM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1../configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2.Make 3.Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4.Make clean This command will clean some files generated during installation which are not needed anymore. 5../configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6.make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8.Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. This is pretty much the standard installation procedure. What we also need to know are the compilers used, etc. for the installation. The error you're getting is from MPICH. Which version is installed on the cluster? It may be old and buggy. In any case, you can try to install something newer, like a recent version of OpenMPI (which we have on our cluster); it may be more reliable. Only a random thought, means nothing unless we know what you have installed :) What about the contents of your system, as I asked before? Do you really have a 100% virtual site system? -Justin Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
RE: [gmx-users] Energies in simulation
Well, I tried to equilibrate the system, and I think the program has
included all the distortion that the system had been through. When I checked
the trajectory, the box was highly distorted as the simulation started, then
returned to its cubic shape. Also, I am a bit confused by the word
strange. Well, based on manual the rvdwrlist and it is. Also, authors in
the paper have tested U with various cutoff radii from 8-11A. The results
were very close! To make sure we are on the same page, the paper address is
J. Chem. Phys., Vol118, No.16 pp7401 (2003).
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:58 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Well, when I set the box, I used 'editconf' command to rescale the box to
have the right density which was ~997. After simulation, I got the
following:
Energy Average RMSD Fluct. Drift
Tot-Drift
---
Density (SI)956.765150.266130.596 0.257477
257.477
The RMSD is very large. Are you sure this is in equilibrium? It could be
that your box is exploding. Please check as well that the strange twin
range cut-off that you are using is what the original authors used.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Here is the content of .itp file which I developed:
; This is an itp file to describe water's six-site model by H. Nada and
J.P.
J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and
3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00
degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name masscharge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.000.00
LW 0.00-0.044 D 0.000.00
[ moleculetype ]
;molnamenrexcl
SOL 1
[ atoms ]
; nratomtyperesnr residuename atomcgnrcharge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OWfunctiondoh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} = Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function 1
;
; site fromfunctiona b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) +
a*(r(i)-r(j))
+
b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} = Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds,
a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} = The denominator is
the
magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site fromfunctiona b c
5 1 2 3 4 -0.437172388-0.437172388
8.022961206
6 1 2 3 4 -0.437172388-0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
And here is the mdp file which I used for the simulation run:
cpp = cpp
include
Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote: Dear Justin, Here is the mpich version: MPICH Version: 1.2.7p1 MPICH Release date: $Date: 2005/11/04 11:54:51$ MPICH Patches applied: none MPICH configure:-prefix=/share/apps/intel/mpich/ MPICH Device: ch_p4 Well, I think that MPICH is your problem then. There are several reports of sporadic bugs (the one that you're seeing!) with that version. Since it's several years old, getting a fix is probably a bit unlikely :) Perhaps you can sort out with the sysadmins what you can do. Like I said before, probably OpenMPI is a better bet - we've never had a problem with it. You can probably install it yourself in your home directory, and point to mpicc with environment variables during the Gromacs installation. Also the gcc compiler: gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9) Copyright (C) 2006 Free Software Foundation, Inc. About the system, I have water model with 3 atom sites and 3 virtual sites. Probably not a very good test case for diagnosing problems, but I think it's unrelated in this case. When testing, keep it simple - run a simulation with spc216.gro from the Gromacs installation, it should pretty much always work :) -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:56 AM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. This is pretty much the standard installation procedure. What we also need to know are the compilers used, etc. for the installation. The error you're getting is from MPICH. Which version is installed on the cluster? It may be old and buggy. In any case, you can try to install something newer, like a recent version of OpenMPI (which we have on our cluster); it may be more reliable. Only a random thought, means nothing unless we know what you have installed :) What about the contents of your system, as I asked before? Do you really have a 100% virtual site system? -Justin Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ gmx-users mailing list
[gmx-users] best way to generate .pdb files?
I am currently using chembiodraw to draw my molecular structure but it does not generate an adequate pdb file. what is the best way to make them? i feel like my only hold back right now is the pdb file. thank you for your help :) _ Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] best way to generate .pdb files?
Joseph Johnson wrote: I am currently using chembiodraw to draw my molecular structure but it does not generate an adequate pdb file. what is the best way to make them? i feel like my only hold back right now is the pdb file. Search the PDB for available ligands, or use the JME editor built into PRODRG. -Justin thank you for your help :) Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Suggestion for g_tune_pme
A small suggested change to g_tune_pme. Allowing the specification of the executable on all the nodes would be appreciated since I (at least) follow the suggestion in the installation directions and suffix my parallel version of mdrun with _mpi, so the executable is mdrun_mpi, not mdrun. You might also want to point out, in the documentation, that one can include the normal mpi commands in the g_tune_pme command. For example, ./g_tune_pme -np 24 -hostfile ethfile24 -s cpeptide_md_PME.tpr works just fine. Jim ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Suggestion for g_tune_pme
Actually, I was incorrect about the use of MPI commands. As a matter of fact, if you don't have your default hostfile set up properly, you will get incorrect results since g_tune_pme will only look at the one node on which you started it. Jim -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Jim Kress Sent: Monday, June 08, 2009 7:20 PM To: 'Discussion list for GROMACS users' Subject: [gmx-users] Suggestion for g_tune_pme A small suggested change to g_tune_pme. Allowing the specification of the executable on all the nodes would be appreciated since I (at least) follow the suggestion in the installation directions and suffix my parallel version of mdrun with _mpi, so the executable is mdrun_mpi, not mdrun. You might also want to point out, in the documentation, that one can include the normal mpi commands in the g_tune_pme command. For example, ./g_tune_pme -np 24 -hostfile ethfile24 -s cpeptide_md_PME.tpr works just fine. Jim ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] zero surface tension
Hello everyone, In the literature, Many reports use the lateral and normal pressures independently coupled to a pressure of 1 bar for bio-membrane simulations. I want to know whether it can guarantee the zero surface tension of the membrane. If not, which situation it can not guarantee. Any suggestion is appreciated. Thanks in advance. -- wende ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with trjconv
Dear all I am on the final step of MD simulation of membrane protein . the final mdrun has successfully completed after that I have filtered the water from the system .next step is to convert it in final pdb to view it in pymol for this I am using trjconv in this step I have to select a group from this option- Group 0 ( System) has 419010 elements Group 1 ( Protein) has 9902 elements Group 2 ( Protein-H) has 7778 elements Group 3 ( C-alpha) has 1000 elements Group 4 (Backbone) has 3000 elements Group 5 ( MainChain) has 4000 elements Group 6 (MainChain+Cb) has 4922 elements Group 7 ( MainChain+H) has 4961 elements Group 8 ( SideChain) has 4941 elements Group 9 ( SideChain-H) has 3778 elements Group10 ( Prot-Masses) has 9902 elements Group11 ( Non-Protein) has 409108 elements Group12 (DMPC) has 5520 elements Group13 ( SOL) has 403578 elements Group14 ( NA+) has10 elements Group15 ( Other) has 409108 elements Select a group: for protein with lipid bilayer which group is suitable can anyone suggest me? Becoz a/c to my opinion in group 0 there may be water also but I want to remove water . so please if anyone have idea about this please suggest me . thanks a lot. Nitu Sharma. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with trjconv
nitu sharma wrote: Dear all I am on the final step of MD simulation of membrane protein . the final mdrun has successfully completed after that I have filtered the water from the system .next step is to convert it in final pdb to view it in pymol for this I am using trjconv in this step I have to select a group from this option- Group 0 ( System) has 419010 elements Group 1 ( Protein) has 9902 elements Group 2 ( Protein-H) has 7778 elements Group 3 ( C-alpha) has 1000 elements Group 4 (Backbone) has 3000 elements Group 5 ( MainChain) has 4000 elements Group 6 (MainChain+Cb) has 4922 elements Group 7 ( MainChain+H) has 4961 elements Group 8 ( SideChain) has 4941 elements Group 9 ( SideChain-H) has 3778 elements Group10 ( Prot-Masses) has 9902 elements Group11 ( Non-Protein) has 409108 elements Group12 (DMPC) has 5520 elements Group13 ( SOL) has 403578 elements Group14 ( NA+) has10 elements Group15 ( Other) has 409108 elements Select a group: for protein with lipid bilayer which group is suitable can anyone suggest me? It seems to me that you haven't actually filtered water, but that you may wish to create a suitable index group. See http://oldwiki.gromacs.org/index.php/Index_File Mark Becoz a/c to my opinion in group 0 there may be water also but I want to remove water . so please if anyone have idea about this please suggest me . thanks a lot. Nitu Sharma. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
