[gmx-users] error about pbc

[Kieu Thu Nguyen]

Thank Tsjerk so much !
But after being minimized 50000 steps and equilibrated 90 ns, there are
some bonds in the system that rotate more than 30 degrees.
I applied tips for blew up system as you advised. But the system does not
achieve balance.
Should i carry out more many steps for minimization ? or minimize many
times ? to get more equilibrated system.

Regards,
KT


On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> Hi KT,
>
> This is caused by another problem. Your system blew up. Check messages
> before this one, and check the log for LINCS warnings.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen <kieuthu2212 at gmail.com
> >wrote:
>
> > Dear All,
> >
> > My MD simulation  has an error
> >
> > Warning: Only triclinic boxes with the first vector parallel to the
> x-axis
> > and the second vector in the xy-plane are supported.
> >          Box (3x3):
> >             Box[    0]={         nan,          nan,          nan}
> >             Box[    1]={         nan,          nan,          nan}
> >             Box[    2]={         nan,          nan,          nan}
> >          Can not fix pbc.
> >
> > I searched on Gromacs-errors web, but i did not see this error.
> > How can i fix it ?
> >
> > Thanks and regards,
> > KT
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
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> Calgary, AB T2N 1N4
> Canada
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