From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Wed Mar 25 2015 - 11:35:27 CDT


In the future, you will get much better advice if you aim these questions
at the official NAMD listserv.

That being said, I think your problem stems from a fundamental
misunderstanding of how NpT and implicit solvent simulations work. The
latter are generally formulated as a grand-canonical muVT ensemble and are
thus wholly incompatible with pressure control. An exception to this would
be the use of a stochastic solvent boundary, but one could argue that that
is not really an implicit solvation approach, but more of a hybrid model.

Hope that helps,

*From:* kathirvel k [k.kathirvel93_at_gmail.com]
*Sent:* Tuesday, March 24, 2015 12:39 AM
*To:* Brian Radak
*Subject:* RE: NAMD

   Hi brain,

 I am also using NAMD for my simulation work ,with implicit solvent model
.and i got some errors in NPT steps ,i think problem occurs in my namd
.conf file only.so pls can you send any example .conf file for implicit
solvent method .am eagerly waiting for your valuable reply

                                               thanking you,

With regards


Sixth year Bioinformatics

School of Life sciences,

Bharathidasan University

Tiruchirappalli-620 024

 Tamil Nadu, India.

Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak_at_uchicago.edu

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