Dear all,<br><br> I have successfully installed the gromacs 4.0.3 it is working but the problem is when I want to run the gromacs demo during processing when I put the command "grompp -v" the output like this ,:-) G R O M A C S (-:<br>
<br> Gromacs Runs On Most of All Computer Systems<br><br> :-) VERSION 4.0.3 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br><br> This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br><br>
:-) grompp (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f grompp.mdp Input, Opt. grompp input file with MD parameters<br>
-po mdout.mdp Output grompp input file with MD parameters<br> -c conf.gro Input Structure file: gro g96 pdb tpr tpb tpa<br> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -n index.ndx Input, Opt. Index file<br> -p topol.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br>
-o topol.tpr Output Run input file: tpr tpb tpa<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br> -e ener.edr Input, Opt. Energy file: edr ene<br><br>Option Type Value Description<br>
------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>-[no]v bool yes Be loud and noisy<br>-time real -1 Take frame at or first after this time.<br>
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br> sites<br>-maxwarn int 0 Number of allowed warnings during input processing<br>-[no]zero bool no Set parameters for bonded interactions without<br>
defaults to zero instead of generating an error<br>-[no]renum bool yes Renumber atomtypes and minimize number of<br> atomtypes<br><br>Ignoring obsolete mdp entry 'title'<br>
Ignoring obsolete mdp entry 'cpp'<br>Ignoring obsolete mdp entry 'domain-decomposition'<br>Replacing old mdp entry 'unconstrained-start' by 'continuation'<br>Ignoring obsolete mdp entry 'dihre-tau'<br>
Ignoring obsolete mdp entry 'nstdihreout'<br>Ignoring obsolete mdp entry 'nstcheckpoint'<br><br>WARNING 1 [file grompp.mdp, line unknown]:<br> Unknown or double left-hand 'bd-temp' in parameter file<br>
<br><br>checking input for internal consistency...<br><br>NOTE 1 [file grompp.mdp, line unknown]:<br> The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.<br>
<br>processing topology...<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp<br>
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp<br>Generated 1284 of the 1485 non-bonded parameter combinations<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>
processing coordinates...<br>double-checking input for internal consistency...<br>Velocities were taken from a Maxwell distribution at 300 K<br>renumbering atomtypes...<br>converting bonded parameters...<br>initialising group options...<br>
processing index file...<br>Analysing residue names:<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>There are: 216 OTHER residues<br>There are: 0 PROTEIN residues<br>There are: 0 DNA residues<br>
Analysing Other...<br>Making dummy/rest group for Acceleration containing 648 elements<br>Making dummy/rest group for Freeze containing 648 elements<br>Making dummy/rest group for Energy Mon. containing 648 elements<br>Making dummy/rest group for VCM containing 648 elements<br>
Number of degrees of freedom in T-Coupling group System is 1293.00<br>Making dummy/rest group for User1 containing 648 elements<br>Making dummy/rest group for User2 containing 648 elements<br>Making dummy/rest group for XTC containing 648 elements<br>
Making dummy/rest group for Or. Res. Fit containing 648 elements<br>Making dummy/rest group for QMMM containing 648 elements<br>T-Coupling has 1 element(s): System<br>Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>
Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>
QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br><br>NOTE 2 [file grompp.mdp, line unknown]:<br> You are using a plain Coulomb cut-off, this will often produce artifacts.<br>
You might want to consider using PME electrostatics.<br><br><br>This run will generate roughly 1 Mb of data<br>writing run input file...<br><br>There were 2 notes<br><br>There was 1 warning<br><br>-------------------------------------------------------<br>
Program grompp, VERSION 4.0.3<br>Source code file: gmx_fatal.c, line: 481<br><br>Fatal error:<br>Too many warnings (1), grompp terminated.<br>If you are sure all warnings are harmless, use the -maxwarn option.<br>-------------------------------------------------------<br>
<br>"How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control) why the grompp -v terminated even i am going step by step as in mannual.<br>could you please anybody tell me about that.<br> Thank you very much in advance.<br>
<br>Nitu sharma<br><br>Structural Biology lab<br>Schoolof Life Sciences <br>Jawaherlal Nehru University<br>New Delhi,India<br><br> <font color="#ffffff"><tt>gmxdump -s topol.tpr | more</tt></font><br><br><br><br><br>