From: Mashayak, Sikandar Yusufoddin (mashaya1_at_illinois.edu)
Date: Wed Jul 10 2013 - 10:43:21 CDT
Hi
I am trying to determine local pressure profiles and surface tension for water liquid-vapor interface.
For that I took a final configuration/coordinate file of a bulk liquid SPC/E water system
GROMACS MD simulation run and increased its Z box dimension to create liquid-vapor interface.
Then generated NAMD pdb, psf, configuration, topology, and force
parameters files by following the NAMD user guide and tutorials. The topology, force field, and
run configuration files are attached.
The problem I am facing is of wrong kinetic part for local pressure tensor (and hence total local pressure) from NAMD. As per my understanding, kinetic part of local pressure, which is written in
the output with tag PPROFILEINTERNAL, should be positive and also follow rho(z)kT relation.
However, the kinetic pressure profile given by NAMD for liquid-vapor water system is negative.
I am not sure what is going wrong here. I am very new to NAMD, may be I am doing something
wrong in my input files.
I will appreciate if anyone can help me to resolve this issue.
Thanks
Sikandar Mashayak
Graduate Research Assistant
Computational Multiscale Nanosystems
University of Illinois at Urbana-Champaign
(http://mashayak.freeshell.net)
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