[gmx-users] Box vector error

[Tsjerk Wassenaar]

Hi Prem,

There is just something terribly wrong with your system if it goes
flat like that. But with only the information you give here, no one
can tell you more than that.

Cheers,

Tsjerk

On Wed, Oct 21, 2009 at 10:18 AM, Prem Singh Kaushal
<ps at mbu.iisc.ernet.in> wrote:
> Dear All
>
>     I am using GROMCS 3.3.1 version. I had started the simulation of protein in
> water with an octahedral box of dimension 9.76276   9.20449   7.97128   0.00000
>  0.00000   3.25425   0.00000  -3.25425  4.60225. However after 25ns the
> simulation aborts with the following error:
>
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or one
> of the box diagonal elements has become smaller than the cut-off.
> The box size at this pint is
>
> At this time point box has changed drastically with vectors,   2.61137  15.10480
>  18.99570   0.00000   0.00000   0.00002   0.00000   0.00002   0.00003.
>
> I tried to restart simulation, going back,  from the time point where there was
> no substantial change in the dimensions of the box, but simulations aborts again
> after some time with the same error. The time points at which simulation aborts
> are random. Having simulated for 25ns now i do not want to change the box shape
> and resimulate everything again.
>
> I shall appreciate you prompt suggestions regarding this.
>
> With regards
> Prem
>
>
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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