[gmx-users] Re: error in grompp for a lipid

Tivadar Orban t.orban at csuohio.edu
Tue Aug 13 04:40:56 CEST 2002

On Monday, August 12, 2002, at 08:25 PM, Erik Lindahl wrote:

> Tivadar Orban wrote:
>> Hi,
>> I tried to simulate a lipid bilayer and when I ran grompp for MD, I 
>> received the following error:
>> processing coordinates...
>> Fatal error: A coordinate in file membrane.gro does not contain a '.'
>> There was no error when I made energy minimisation an position 
>> restraint molecular dynamics.
>> Could somebody give me a hint what this error could mean?
>> Regards
>> Tivadar, Orban
> Hi,
> Check the contents of the membrane.gro file - you might have had a bad 
> contact that resulted in a numerical error (causing a NaN value instead 
> of coordinate).
> Cheers,
> Erik

Thanks Erik for your fast reply.
I checked the membrane.gro file but there isn't  any NaN value. Could be 
something else wrong? I built up the lipid bilayer with an algorithm, 
starting from a lipid, because  I needed a lipid bilayer with a given 
surface. Can it be that  the model works fine for energy minimization, 
position restraint but not for the MD part?

Tivadar, Orban

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