[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


g_select can be used to extract the number of TFE molecules around a given residue at each frame.


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.


Dra. Adriana D. Garro
Química Medicinal
Facultad de Química, Bioquímica y Farmacia
Universidad Nacional de San Luis
San Luis, Argentina

Tel..............:+54 266 4424689  int 6153
e-mail...: adgarro at unsl.edu.ar
e-mail...:  adrianagarrosl at gmail.com

Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list