[gmx-users] Re Re: Error 1-4 interaction

[Maarten Wolf]

From: Anton Feenstra 
Subject: Re: [gmx-users] error 1-4 interaction
Date: Thu, 22 Jul 2004 10:49:55 +0200
To: Discussion list for GROMACS users 

Maarten Wolf wrote:

> Hello,
> 
> I am running simulations on a protein/water system. Until now I used cut-off for both the coulomb as the VdW interactions. However I am wondering if the Coulomb Cut-off is appropriate for my system. So I performed a simulation using PME. It starts all fine but after app 25000 steps of 0.002 ps I get the following error message:
> 
> Warning: 1-4 interaction between 272 and 275 at distance larger than 1.9
> nm These are ignored for the rest of the simulation turn on -debug for
> more information Wrote pdb files with previous and current coordinates
> /var/spool/PBS/mom_priv/jobs/42397.ruben.SC: line 2: 17951 Segmentation
> fault mdrun -s topol.tpr
> 
> Can anybody explain to me what this error means?

Probably your system is exploding. Look at energies and/or conformations.
You may want to increase nstener or nstxtcout, and/or set LOGBUFS = 0 to
turn of buffering of file output.


I checked the energies of my system as well as the conformations for the first 44 frames (22000 steps) the energies are constant upto this point and nothing unusual is seen for the conformations. Nevertheless I will perform a simulation with increased number of output



-- 
Groetjes,

Anton
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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Groetjes Maarten

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