[gmx-users] SASA with rhombic dodecahedron

rajat desikan rajatdesikan at gmail.com
Mon Nov 10 14:29:21 CET 2014


Hi Tsjerk,

Is this the resolved g_sas issue that you were alluding to?
http://redmine.gromacs.org/issues/1445

I don't know if it is the solution to using a non-rectangular box. SASA
calculations form an integral part of my conclusions, and I would like to
be sure about their calculation. Thanks.

Regards,

On Mon, Nov 10, 2014 at 6:36 PM, rajat desikan <rajatdesikan at gmail.com>
wrote:

> 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.
>> --
>> Gromacs Users mailing list
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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
>



-- 
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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