<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks for your reminder!<br><br>javacfish<br>---------------------------------------------------<br>li<br><br>i think if you use -maxwarn 1, that's fine only for this time only.<br>Actually you will also get the same prob later at the when using posre.mdp and also mdrun.mdp ..if you still you the old mdp file.<br>the best way, you should have the new mdp which is generated as an output after you run the grompp<br><br>anyway..all the best<br><br>On Tue, Mar 10, 2009 at 4:06 PM, li bai <javacfish@yahoo.com.cn> wrote:<br><br><br> I have resolved the problem,please see:<br> http://www.gromacs.org/pipermail/gmx-users/2008-November/038056.html<br><br> Add the "grompp -v -maxwarn 1", That is ok!<br><br> I think there is possible something wrong to<br> the .mdp file. That
is not necessary in the gromacs 3.x,<br> but not in gromacs 4.x.Gromacs 4.x check every err in every step!<br><br> Thanks all!<br> --- On Tue, 3/10/09, sitiazma <sitiazma@gmail.com> wrote:<br><br><br> From: sitiazma <sitiazma@gmail.com><br> Subject: Fwd: gmx-users Digest, Vol 59, Issue 74<br> To: javacfish@yahoo.com.cn<br> Date: Tuesday, March 10, 2009, 9:04 PM<br><br><br> I think your problem below because you are using old mdp file for new gromacs 4.<br><br> so now you should rename the mdout.mdp to new.mdp<br> and you need to change the below line from berendson to
V-rescale<br><br> ; OPTIONS FOR WEAK COUPLING ALGORITHMS<br> ; Temperature coupling<br> tcoupl = V-rescale<br><br> good luck<br><br> Siti<br><br> Message: 2<br> Date: Tue, 10 Mar 2009 17:32:39 +0800 (CST)<br> From: li bai <javacfish@yahoo.com.cn><br> Subject: [gmx-users] "Gromacs 4 grompp -v" err<br> To: gmx-users@gromacs.org<br> Message-ID:
<117928.54707.qm@web15005.mail.cnb.yahoo.com><br> Content-Type: text/plain; charset="utf-8"<br><br> Hello,everyone!<br> Sorry for the last letter!<br> I have install gromacs4, but when I stury the tutor of gromacs, and input command "grompp -v in every examples", the err be engenderred as below:<br><br> li@localhost water]$ grompp -v<br> :-) G R O M A C S (-:<br><br> Go
Rough, Oppose Many Angry Chinese Serial killers<br><br> :-) VERSION 4.0.4 (-:<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 http://www.gromacs.org 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> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<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 /home/bai/workdir/gromacs4/share/gromacs/top/ffgmx.itp<br> Opening library file /home/bai/workdir/gromacs4/share/gromacs/top/ffgmxnb.itp<br> Opening library file /home/bai/workdir/gromacs4/share/gromacs/top/ffgmxbon.itp<br> Opening library file /home/bai/workdir/gromacs4/share/gromacs/top/ff_dum.itp<br> Opening library file /home/bai/workdir/gromacs4/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 /home/bai/workdir/gromacs4/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, which might 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 4.0.4<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><br> Who can help me to solve this problem?<br></td></tr></table><br>