[gmx-users] Energy Calculation
Hi! I want to calculate energy from GROMOS96-GB/SA. What command should be used? -- 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] Normal mode analysis of pure water
Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx nm.mtx Getting Loaded... Reading file water.tpr, VERSION 4.0.4 (double precision) Loaded with Money Non-cutoff electrostatics used, forcing full Hessian format. Allocating Hessian memory... starting normal mode calculation 'Pure Water' 648 steps. Maximum force: 2.74758e+03 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. Finished step 648 out of 648 Writing Hessian... gcq#258: In the End Science Comes Down to Praying (P. v.d. Berg) g_nmeig_d -f nm.mtx -s water.tpr -of eigenfreq.xvg -ol eigenval.xvg -v eigenvec.trr Reading file water.tpr, VERSION 4.0.4 (double precision) Reading file water.tpr, VERSION 4.0.4 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.0.4 Full matrix storage format, nrow=1944, ncols=1944 Diagonalizing to find vectors 1 through 50... One of the lowest 6 eigenvalues has a non-zero value. This could mean that the reference structure was not properly energy minimized. Writing eigenvalues... Writing eigenfrequencies - negative eigenvalues will be set to zero. Writing average structure eigenvectors 1--50 to eigenvec.trr gcq#132: Shit Happens (Pulp Fiction) The eigenfreq is 0 which is the problem The .mdp file used was; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = define = -DFLEXIBLE constraints = none integrator = nm nsteps = 1 ; ; Energy minimizing stuff ; emtol = 0.01 emstep = 0.01 coulombtype = PME nstcomm = 1 ns_type = grid rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 Tcoupl = no Pcoupl = no gen_vel = no ___ 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] Normal mode analysis of pure water
Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. ___ 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] Normal mode analysis of pure water
Hi Berk, You mentioned that standard NMA techniques will not work for the liquid water system. Could you suggest the alternatives then? ___ 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] Normal mode analysis of pure water
Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What extension would the file have (.what) ? ___ 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] multiple T-Coupling groups
Hi, I used the followng command and encountered an error. Can someone please offer a solution. grompp -f grompp.mdp -n index.ndx -p topl.top -c conf.gro -o water.tpr :-) G R O M A C S (-: Green Red Orange Magenta Azure Cyan Skyblue :-) VERSION 4.0.4 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f grompp.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c conf.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt! Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -o water.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Ignoring obsolete mdp entry 'domain-decomposition' Replacing old mdp entry 'unconstrained-start' by 'continuation' WARNING 1 [file grompp.mdp, line unknown]: Unknown or double left-hand 'zero-temp_time' in parameter file checking input for internal consistency... WARNING 2 [file grompp.mdp, line unknown]: epsilon_r = 0 and epsilon_rf = 1 with reaction field, assuming old format and exchanging epsilon_r and epsilon_rf processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Generated 1284 of the 1485 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... --- Program grompp, VERSION 4.0.4 Source code file: readir.c, line: 1058 Fatal error: Atom 1 in multiple T-Coupling groups (1 and 2) --- Wild Pointers Couldn't Drag Me Away (K.A. Feenstra) ___ 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] Normal mode analysis
Hi! I am a user of gromacs. Could someone provide me with a method (or set of commands) for normal mode analysis of small molecules (water, n-butane, etc). Also could you please provide a command for generating Hessian Matrix after the energy minimization. ___ 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 create topology file for butane
Respected sir, I am working on GROMACS. I need your help.I am trying to generate topology file for non-standard molecules like butane, water. I am executing following command. *pdb2gmx -f ALA.pdb -p ALA.top -o ALA.gro* ** It is successfully working on amino acid residue. But when i am executing it for butane. *pdb2gmx -f BUTANE.pdb -p BUTANE.top -o BUTANE.gro* ** ** Fatal error: Residue 'DRG' not found in residue topology database It is showing above errors.Please help me out on this. ___ 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
