Re: [ESPResSo] basic details:

[Christopher Jesudason]

Thank you for replying. Just two  points:
1)In the paper by Arnold et al. on the Espresso
package at the acknowledgment section  , it speaks of
the need for improvement based on teamwork based on 
user feedback etc.. for there to be improvements. I
write as a beginning user giving  this type of
feedback with the view of making things a little
clearer for other potential users who are just
starting out. I have read Tildesley, written my own
MD, published papers   and also wrote a paper in
Nonlinear Analysis on a mathematical theory of
scientific equations and units, presenting a vector
space model. I was intrigued when I read through the
MDIONS2 program given on the web by the Daresbury
laboratory by Anastasios and D Fincham where the
scaling was done in such a way that the time
difference interval was always unity, and that is not
simply by choice but by the method used, which was
very interesting;in that sense a little inclusion of
the method of scaling might reduce ambiguity in
Espresso; i.e. you might say that the Daresbury group
method was not used and perhaps mention that the
standard Tildesley method with t as a free parameter
was employed.
2) Concerning the Langevin thermostat, I did refer to
the two articles on the Espresso package that
mentioned these , but the possible references to the
thermostats refer to DPD and to many other references
like a tree diagram without exact pinpointing. Do you
mean that the Berendsen method was used?; even here,
the method (which is essentially Langevin) is coupled
to the details of the Verlet type algorithm, and the
\tau  parameter or gamma parameter must be defined
within the scheme of equations used . I noticed that
there is a more detailed writeup of the  potentials
used in your User guide, but a similar brief
description of the thermostat and the connection to
the  Verlet algorithm and the gamma parameter would be
helpful; if space does not permit, then perhaps an
exact reference to  a paper with the equation number 
might help some of us or else it would appear to be a
black box for some of us.
Thanks, Chris 


      
____________________________________________________________________________________
Fussy? Opinionated? Impossible to please? Perfect.  Join Yahoo!'s user panel 
and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7