[gmx-users] mdrun error after 2.6nS

[Tsjerk Wassenaar]

Hi Blaise,

Check for the first occurrence of the error in the log file and match the
atom numbers against your .gro file to see which residue is involved from
the beginning. Also, do you have non-standard residues/metal ions? Tell more
about the system and what you're trying to do.

Best,

Tsjerk

On 10/3/07, Blaise Mathias-Costa <bmathiascosta at unmc.edu> wrote:
>
> 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
>
> -----gmx-users-bounces at gromacs.org wrote: -----
>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Sent by: gmx-users-bounces at gromacs.org
> 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
> _______________________________________________
> 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
>
>
>
> _______________________________________________
> 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
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071003/f2b86793/attachment.html>