[gmx-users] Distribution of the TFE/Water molecules around a peptide

[Smith, Micholas D.]

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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