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 <[EMAIL PROTECTED]> wrote:
Dear Gromacs users,
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).
Regards,
Gurpreet Singh
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
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