[gmx-users] simulation of a peptide anchored to a support

Anna Marabotti anna.marabotti at isa.cnr.it
Thu May 19 11:09:58 CEST 2011

Dear gmx-users,
I would like to simulate the conformational behaviour of a peptide
covalently anchored to a rigid support with its N- and C-ter. I'm not
interested in simulating the support, so I wonder if there is a way to
simulate the peptide with its N- and C-ter fixed. Could freezegrps work for
this? Otherwise (or in addition) could I fix the peptide on one side of the
simulation box, in order to avoid the fluctuation of the peptide into the
solvent? Finally, do I have to add special constraints/restraints to my
Any suggestion will be appreciated, many thanks in advance
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabotti at isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with a gun is a dead
(Roberto Benigni, about Roberto Saviano)
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