[gmx-users] Distribution of the TFE/Water molecules around a peptide
Smith, Micholas D.
smithmd at ornl.gov
Mon Aug 10 17:26:20 CEST 2015
Adriana,
g_select can be used to extract the number of TFE molecules around a given residue at each frame.
-Micholas
===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Adriana Garro <adrianagarrosl at gmail.com>
Sent: Monday, August 10, 2015 11:14 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Distribution of the TFE/Water molecules around a peptide
Dear users,
My system is a peptide surrounded by TFE and water molecules. Since
bibliography I can expect a preferential aggregation of TFE molecules
around the peptide, after a 20 ns simulation and using VMD this effect is
not obvious, but of course, I should analize more, for example the relative
number of solvent molecules within a cutoff distance around each residue.
Could you please recommend me some Gromacs tool to do that?
Thank in advance.
Adriana
***********************************************************
Dra. Adriana D. Garro
Química Medicinal
Facultad de Química, Bioquímica y Farmacia
Universidad Nacional de San Luis
IMASL-CONICET
San Luis, Argentina
Tel..............:+54 266 4424689 int 6153
e-mail...: adgarro at unsl.edu.ar
e-mail...: adrianagarrosl at gmail.com
**********************************************************
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