[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] 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] 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
[gmx-users] about epsion_surface
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. -- 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] how to run with mpi?
i have a small cluster of 3 computers, 1 master and 2 slaves, running Rocks 4.2.1 and Gromacs 3.3.1. Are there any good tutorials about how to use openmpi and Gromacs? I'm rather new to this so any help would be amazing. Thank you :) _ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009___ 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] Scaled 1-5 interactions
On Sun, Jun 07, 2009 at 05:35:14PM +0200, Florian Dommert wrote: > Glad to hear the my help works. Setting the LJ parameters zero for the > should avoid a further contribution of the LJ part from the defined 1-5 > IA, since they are already present in the nonbonded part of the > interaction types. Accoring to Chapter 5.3.4 of the manual, the [ pairs ] > directive allows to add further nonbonded energy terms within a molecule. > This is exactly the goal we want to achieve ;) Ah, yes. You are right :-) I think, I've got finally the hang of all these parameters. Borys -- REQUIMTE, & Molecular Modelling & Quantum Chemistry Group, Department of Chemistry, & Institute of Physical & Theoretical Chemistry, Faculty of Science, & Wroclaw University of Technology University of Porto & http://ichfit.ch.pwr.wroc.pl/people/szefczyk ___ 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] Scaled 1-5 interactions
* Borys Szefczyk [2009-06-07 14:12:14 +0200]: On Sat, Jun 06, 2009 at 02:06:56PM +0200, Florian Dommert wrote: * David van der Spoel [2009-06-06 08:06:26 +0200]: The VDW may work, but not differently scaled 1-4 and 1-5 coulomb interactions. Where is the matter if I have a [ pairs ] directive in the itp file like this : [ pairs ] ; ai aj fu 15 2 0.5 -0.11 0.13 0.30250 0.095865 16 2 0.5 -0.11 0.13 0.30250 0.095865 . . . . ;this is are nonbonded intramolecular IAs separated by more than theree bonds 2 5 2 7.569 0.07200 0.02300 0.0 0.0 2 6 2 7.569 0.07200 0.02300 0.0 0.0 I think this will work, but setting LJ parameters to zero will cancel the interaction for these pairs. Is this what you intend to do? Glad to hear the my help works. Setting the LJ parameters zero for the should avoid a further contribution of the LJ part from the defined 1-5 IA, since they are already present in the nonbonded part of the interaction types. Accoring to Chapter 5.3.4 of the manual, the [ pairs ] directive allows to add further nonbonded energy terms within a molecule. This is exactly the goal we want to achieve ;) Cheers, Flo I did a simple test: I've defined an abstract molecule like this: X-X-X-X-X so that 1 and fourth atom are 0.4 nm apart, and 1 and fifth atom are 0.5 nm apart. I've set all bonded and non-bonded interactions to zero, Nexcl=3, gen-pairs=yes, fudgeQQ=1.0, fugdeLJ=1.0. Then I have defined [pairs] like this: [ pairs ] 1 4 2 1.0 0.1 0.0215927 0.3250520.25 1 5 2 1.0 0.1 0.0287903 0.4334020.25 charges, sigma and epsilon are chosen in such a way that each interaction should contribute exactly 1 kJ/mol. Indeed, the potential energy calculated by GROMACS is 4 kJ/mol. Now, changing the pairs to: [ pairs ] 1 4 2 0.5 0.1 0.0215927 0.3250520.25 1 5 2 0.8 0.1 0.0287903 0.4334020.25 I get the potential energy of 3.3 kJ/mol, which means that coulomb14 whas rescaled from 1 to 0.5 and coulomb15 was rescaled from 1 to 0.8. This is exaclty what I was looking for. Thanks for all the comments, Borys -- REQUIMTE, & Molecular Modelling & Quantum Chemistry Group, Department of Chemistry, & Institute of Physical & Theoretical Chemistry, Faculty of Science, & Wroclaw University of Technology University of Porto & http://ichfit.ch.pwr.wroc.pl/people/szefczyk ___ 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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !! pgpD2thzLyKbM.pgp Description: PGP signature ___ 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] reg aCTIVE SITE
Quoting vidhya sankar : > Dear gromacs users, > Is there is any tools available in > gromacs to predict active site of protein molecule ? othewise how could we > predict active site of a protein molecule > please let me know . i am waitingfor your positive reply > There is no Gromacs tool, but this is a standard application of bioinformatics techniques (sequence analysis/alignment). -Justin > > Bollywood news, movie reviews, film trailers and more! Go to > http://in..movies.yahoo.com/ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] reg aCTIVE SITE
Dear gromacs users, Is there is any tools available in gromacs to predict active site of protein molecule ? othewise how could we predict active site of a protein molecule please let me know . i am waitingfor your positive reply Bollywood news, movie reviews, film trailers and more! Go to http://in..movies.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] Scaled 1-5 interactions
On Sat, Jun 06, 2009 at 02:06:56PM +0200, Florian Dommert wrote: > * David van der Spoel [2009-06-06 08:06:26 +0200]: >> The VDW may work, but not differently scaled 1-4 and 1-5 coulomb >> interactions. > > Where is the matter if I have a [ pairs ] directive in the itp file like > this : > > > [ pairs ] > ; ai aj fu > 15 2 0.5 -0.11 0.13 0.30250 0.095865 > 16 2 0.5 -0.11 0.13 0.30250 0.095865 > . > . > . > . > ;this is are nonbonded intramolecular IAs separated by more than theree > bonds > 2 5 2 7.569 0.07200 0.02300 0.0 0.0 > 2 6 2 7.569 0.07200 0.02300 0.0 0.0 I think this will work, but setting LJ parameters to zero will cancel the interaction for these pairs. Is this what you intend to do? I did a simple test: I've defined an abstract molecule like this: X-X-X-X-X so that 1 and fourth atom are 0.4 nm apart, and 1 and fifth atom are 0.5 nm apart. I've set all bonded and non-bonded interactions to zero, Nexcl=3, gen-pairs=yes, fudgeQQ=1.0, fugdeLJ=1.0. Then I have defined [pairs] like this: [ pairs ] 1 4 2 1.0 0.1 0.0215927 0.3250520.25 1 5 2 1.0 0.1 0.0287903 0.4334020.25 charges, sigma and epsilon are chosen in such a way that each interaction should contribute exactly 1 kJ/mol. Indeed, the potential energy calculated by GROMACS is 4 kJ/mol. Now, changing the pairs to: [ pairs ] 1 4 2 0.5 0.1 0.0215927 0.3250520.25 1 5 2 0.8 0.1 0.0287903 0.4334020.25 I get the potential energy of 3.3 kJ/mol, which means that coulomb14 whas rescaled from 1 to 0.5 and coulomb15 was rescaled from 1 to 0.8. This is exaclty what I was looking for. Thanks for all the comments, Borys -- REQUIMTE, & Molecular Modelling & Quantum Chemistry Group, Department of Chemistry, & Institute of Physical & Theoretical Chemistry, Faculty of Science, & Wroclaw University of Technology University of Porto & http://ichfit.ch.pwr.wroc.pl/people/szefczyk ___ 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
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+011.40158e+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+011.44270e+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+011.43458e+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+011.44419e+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+011.46722e+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+011.46338e+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+011.45770e+03 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 3.07425e+03 -2.71320e+04 -2.21700e+044.17285e+03 -1.79972e+04 Temperature Pressure (bar) Cons. rmsd () 3.13281e+025.60002e+011.97532e-05 DD step 699 vol min/aver 0.664 load imb.: force 13.1% ---
