[gmx-users] SASA with rhombic dodecahedron

[rajat desikan]

Thank you, Tsjerk. I will take a look. Are there any compatibility issues
with a 4.6.4 trajectory and GMX 5 analysis tools?

On Mon, Nov 10, 2014 at 4:04 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Rajat,
>
> Maybe try GMX 5. It appears this was fixed.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Nov 10, 2014 at 9:49 AM, rajat desikan <rajatdesikan at gmail.com>
> wrote:
>
> > Dear All,
> >
> > SASA calculations of a solvated protein in a rhombic dodecahedron gives
> the
> > following warning:
> >
> > WARNING: non-rectangular boxes may give erroneous results or crashes.
> > Analysis based on vacuum simulations (with the possibility of
> evaporation)
> > will certainly crash the analysis.
> >
> > Is there any way to go about this? Repeating the simulation is
> > unfortunately not an option. Thanks.
> >
> > Regards,
> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore