Re: [gmx-users] mdrun error after 2.6nS

[Blaise Mathias-Costa]

Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after 2.6nS!

I have searched in the archive, when somebody had similar problem with PR run David suggested to look for the "center-of-mass motion removal", to give POPC+Protein, but I dont have POPC in my system. In another case advised to reduce the time step, does it mean that I should reduce the time step from 0.002 to 0.001 and do the simulations from the beginning?

 

Another suggestion was the computing power may not be sufficient, but I don't think this will be applicable for me, b'se I am running in 8 nodes each node is with 4 processors, and the unit cell size is ~96000 atoms in total.

 

What could be the most appropriate way to solve this problem?  Many thanks in  advance!

 

Kind Regards,

Blaise

Blaise Mathias Costa, PhD
Department of Pharmacology and Experimental Neuroscience
University of Nebraska Medical Center
Omaha, NE 68198-5800, USA.
Tel: 001 402 559 7132 

[EMAIL PROTECTED] wrote: -----

To: Discussion list for GROMACS users <gmx-users@gromacs.org>
From: Mark Abraham <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
Date: 10/02/2007 12:29PM
Subject: Re: [gmx-users] mdrun error after 2.6nS

Blaise Mathias-Costa wrote:
> Hi all,
>
> The mdrun stopped  after 2.6nS  after writing this error:
> Step 1321571, time 2643.14 (ps)  LINCS WARNING

See http://wiki.gromacs.org/index.php/Errors#LINCS_warnings

Mark
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