Dear Giovanni Pavan,
Currently, pmemd nor pmemd.cuda does not support a NPT simulation where the periodic box changes in only one direction.
Looking at the Amber manual, setting NPT = 2 will allow the pressure in your system to vary anisotropically, but all the periodic box dimensions are allowed to change.
Ross Walker and I have recently added a constant surface tension option for NPT = 2 in pmemd that should be available in the next release of Amber. This will be available for systems with interfaces (like lipid bilayers). In constant surface tension simulations, the pressure regulation has an additional constraint from a set surface tension value.
Constant area simulations would not be too difficult to implement into the current pressure regulation code in pmemd.
Are you running an interfacial system like a lipid bilayer?
Ben Madej
Walker Molecular Dynamics Lab
University of California, San Diego; San Diego Supercomputer Center
________________________________________
From: Giovanni Pavan [giovanni.pavan.supsi.ch]
Sent: Saturday, November 05, 2011 11:16 AM
To: amber.ambermd.org
Subject: [AMBER] anisotropic NPT simulation
Dear all,
is it possible to run an NPT simulation where the periodic box (and thus the
pressure) is allowed to change only in one direction - i.e. along the
Z-axis?
I would like to do that using pmemd.cuda: is it possible? How?
I thank you in advance for your feedback.
Bye
Giovanni
Dr. Giovanni Maria Pavan
SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI)
Centro Galleria 2, Manno 6928, Switzerland.
e-mail: giovanni.pavan.supsi.ch
skype: giovanni_pavan
phone: +41 58 666 65 60
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 05 2011 - 18:00:03 PDT
