[gmx-users] errors position restraints in a linux cluster

David spoel at xray.bmc.uu.se
Tue Sep 28 22:40:17 CEST 2004

On Tue, 2004-09-28 at 22:07, gerph at correo.unam.mx wrote:
> Dear all,
> recently, I get access to a linux-cluster in my university to run gromacs,
> however, after a few days of test, with errors, I saw that the administers
> installed gromacs 3.1.1. Previusly I did a test with my protein in a single
> linux workstation with gromacs 3.2.1 without problems and then I tried run the
> same MD steps in the cluster but I am having the next problem with position
> restraints and Na,
> Back Off! I just backed up mdout.mdp to #mdout.mdp#
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> WARNING 1 [file /home/inv/evqz/beta/300K/pr.mdp, line unknown]:
>   Can not do sorting without shuffling. Sorting turned off.
> Excluding 3 bonded neighbours for Protein_E 1
> Excluding 1 bonded neighbours for SOL 27509
> Excluding 1 bonded neighbours for Na 20
> processing coordinates...
> Reading file /home/inv/evqz/beta/300K/tbeta_em.tpr, VERSION 3.1.1 (single precision)
> Reading file /home/inv/evqz/beta/300K/tbeta_em.tpr, VERSION 3.1.1 (single precision)
> Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> /home/inv/evqz/beta/300K/tbeta_em.tpr don't match (OW - Na)
> Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> /home/inv/evqz/beta/300K/tbeta_em.tpr don't match (HW1 - Na)

This is a serious error, but easy to fix. The order of the atoms in the
topology is not the same as in the coordinate file. You probably have
ions first in one of the files, and water first in the other. Edit the
top file with a text editor.

> its look the same for the rest of Na
> I am using gromacs force field and I add #include "ions.itp" in the top file as
> well as I arranged the lines of n ions by solvent before run grompp.
> I need upgrade to 3.2.1?
> I appreciate any insights about this problem. 
3.2.1 contains quite a few bug fixes, but we will also release 3.3.0
*real soon now* so it may be good to wait a couple of days..

> Thanks in advance,
> Gerardo Pérez-Hernández
> -------------------------------------------------
> www.correo.unam.mx
> UNAMonos Comunicándonos
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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