[gmx-users] Aggregation Analysis

Smith, Micholas D. smithmd at ornl.gov
Fri Sep 21 15:28:16 CEST 2018

You may be able to use gmx clustsize to do this, but it may require some careful atom-selections.


Micholas Dean Smith, PhD. MRSC
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 Aishwarya Dhar <dhar.aishwarya at gmail.com>
Sent: Friday, September 21, 2018 9:02 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Aggregation Analysis

Dear Gromacs users,

I want to classify some peptide aggregates in my simulation box,
I'd like to know which are the atoms belonging to each 'aggregate' to
study the aggregate shapes.

Is there any gromacs tool suitable for this purpose?
the best will be to select the atoms according to some kind of
distance cut-off and then to print an index file containing the list
of the atomic number for each of the aggregate.

Thank you in advance,
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