[gmx-users] mdp file to calculate local pressure

Justin A. Lemkul jalemkul at vt.edu
Sat May 23 12:41:13 CEST 2009

anirban polley wrote:
> Dear Sir,
>              I am looking for local pressure where I am using 
> gromacs-4.0.2_localpressure.tar 
> <ftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gz> 
> package. I have download it from
>                                    ftp://ftp.gromacs.org/pub/tmp
> The error which it gives during running to make tpr file, is given below
> -------------------------------------------------------
> Program grompp_mpi, VERSION 4.0.2_localpressure
> Source code file: gmx_fatal.c, line: 481
> Fatal error:
> Too many warnings (1), 
> /home/anirban/gromacs402localpressure/bin/grompp_mpi terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> -------------------------------------------------------
> The warning which it gives during running to make tpr file, is given below
> WARNING 1 [file popc-sm-chol-assymmetric-bilayer.top, line unknown]:
>  The largest charge group contains 11 atoms. 
> Since atoms only see each other when the centers of geometry of the charge
> groups they belong to are within the cut-off distance, too large charge
>  groups can lead to serious cut-off artifacts.
>  For efficiency and accuracy, charge group should consist of a few atoms.
>  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
> Sir, now, could you please tell me where I have done mistake? In the 
> README file, it is written that it will give localpressure.dat file 
> automatically. But I could not do it.

The error message is clear.  You have a charge group containing 11 atoms, which 
is far larger than charge groups normally are.  Revise your parameters to give 
something more reasonable.  If you are comfortable with the 11-atom charge 
group, then increase the -maxwarn option, as grompp has told you.


> Thank you very much for you kind help,
> Anirban Polley
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list