Re: [gmx-users] energy minimization error
On 5/16/15 6:27 AM, James Lord wrote: Dear gmx users, I am getting this error, Can anyone help me to get around this? Cheers James Program mdrun, VERSION 4.6.3 Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.93203 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition Log file opened on Sat May 16 22:15:44 2015 Host: james-E530 pid: 22300 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Wed Oct 30 18:28:46 NZDT 2013 Built by: james@james-E530 [CMAKE] Build OS/arch: Linux 3.11.0-12-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1 C compiler flags: -mavx-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- Input Parameters: integrator = steep nsteps = 5 init-step= 0 cutoff-scheme= Group ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 100 comm-mode= Linear nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy= 100 nstenergy= 1000 nstxtcout= 0 init-t = 0 delta-t = 0.001 xtcprec = 1000 fourierspacing = 0.12 nkx = 56 nky = 56 nkz = 144 pme-order= 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface
Re: [gmx-users] warnings in energy minimization
On 5/16/15 12:14 AM, James Lord wrote: Hi all, I am using Justin's minim.mdp to energy minimize my system and I am getting these warnings,Should I care about them? It is saying that my simulation may not be stable? Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 WARNING: Listed nonbonded interaction between particles 5312 and 5315 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] question
Dear Tsjerk residue numbers in chain B are as 220-434. GLU residue is 380. residue numbers in chain E are as 435-551. LYS residue is 540. How to merge these two chains through these two residues? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] position restraints
On 5/16/15 8:13 AM, Ming Tang wrote: Dear all, I want to minimize my system to relax the solvent with the positions of heavy atoms within the protein restrained. I searched the archives and got the idea that I need to put something like this in topology: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif But I still have no idea how to get the heavy atoms restrained. Could anybody tell me how to do this? pdb2gmx does this automatically for you. It writes posre.itp, which specifies heavy atom restraints. It's controlled by a similar #ifdef block. I want to use gromos54a7 ff to simulate my collagen. As Justin suggested, I need to study the original paper Definition and testing of the GROMOS force-field versions 54A7 and 54B7 to write my .mdp file. In the paper it says, 1. Each system was energy minimised to relax the solvent with the positions of the heavy atoms within the protein and RNA restrained. 2. All solute atom positions were restrained to their positions in the initial structure through a harmonic potential energy term with force constant of 2.5 9 104 kJ mol-1 nm-2. Could anybody tell me how to restrain the heavy atoms of protein, and how to get the solute atom positions restrained with a harmonic potential energy term with a certain constant? This is what posre.itp does. Also note that you don't necessarily have to follow that protocol exactly; my general advice for proper use of force fields is about proper nonbonded setup. Preparation of a system often depends on what the system is and if there are any special considerations. For a simple protein system, it's pretty hard to break things. I don't see much benefit in restraining atoms during minimization, though. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] question
Dear Tsjerk I used pdb2gmx -f be_near.pdb -ignh -merge Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
