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[ESPResSo] Visualisation of MD trajectories - assigning of angle and dih
From: |
Marek Maly |
Subject: |
[ESPResSo] Visualisation of MD trajectories - assigning of angle and dihedral parameters - rdf over more configs ? |
Date: |
Tue, 06 Apr 2010 00:48:36 +0200 |
User-agent: |
Opera Mail/10.10 (Win32) |
Dear Espresso users,
I have 3 questions.
#1
Currently there are problems with the visualisation of VTF trajectories
using VMD under
some Windows versions. Please see this thread:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15575.html
So I would like to know, if there is any other possibility how to
visualise MD trajectory from Espresso calculation ?
#2
Is in actual Espresso possible to set angle and dihedral parameters just
using
particle types of bonded particles similarly like in atomistic forcefields
are predefined these parameters
according to the atom types of the bonded triplet or quaternion of atoms ?
Let say that I have particles of type 0 and 1 in my system. It is possible
to define "globally" angle parameters
for all the relevant combinations of bonded particle types:
0-0-0, 0-0-1, 0-1-0 , 1-0-1, 1-1-1 (for angle parameter setting)
or
0-0-0-0, 0-0-0-1 ... (for dihedral parameters)
#3
Is there available exmple of Espresso calculation where the
analyze <rdf>
command is used to calculate radial distribution function averaged over
previously stored configurations ?
Is it really necessary to store configurations in files to calculate <rdf>.
I mean is it possible to calculate <rdf> during simulation from
let say last N loops of the INTEGRATE "for" cycle (of course without my
own tcl coding).
Thank you very much for any relevant comment.
Best wishes,
Marek