[gmx-users] do_dssp

[Tsjerk Wassenaar]

Hi Gurpreet,

The common message is "don't worry, mdrun doesn't write broken
molecules". So you're secondary structure will not be affected by
periodic boundary conditions.

Cheers,

Tsjerk

On 12/21/06, singh <singh at biophysik.chemie.uni-dortmund.de> wrote:
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> Dear Gromacs users,
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> I have simulated 12 peptide fragments in a cubic box and I want to use
> do_dssp for secondary structure analysis but I am not sure whether Periodic
> boundary conditions will be taken in account during assignment (particularly
> for assigning betasheets).
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> Regards,
>
> Gurpreet Singh
>
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-- 
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