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

[Anna Marabotti]

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
molecule?
Any suggestion will be appreciated, many thanks in advance
Anna
 
____________________________________________________
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
man"
(Roberto Benigni, about Roberto Saviano)
 
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