From: Jiao, Dian NMN (-EXP) (dnjiao_at_sandia.gov)
Date: Fri Nov 04 2011 - 17:38:56 CDT
The equilibrated system at 600k would probably have a much larger volume than 300k. Ultimately, I will run REMD at different temperatures. In order to make the replica exchange, the two neighboring simulations should have the same volume. Is that right? Or in REMD, I should fix the size of the water box regardless of the system temperature?
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>>
Date: Fri, 4 Nov 2011 17:56:12 -0400
To: Dian Jiao <dnjiao_at_sandia.gov<mailto:dnjiao_at_sandia.gov>>
Cc: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>
Subject: Re: namd-l: membrane simulation at high Temp
Perhaps constant volume?
On Fri, Nov 4, 2011 at 5:50 PM, Jiao, Dian NMN (-EXP) <dnjiao_at_sandia.gov<mailto:dnjiao_at_sandia.gov>> wrote:
I was trying to run simulations for an ion channel embedded in a lipid bilayer. With constant area restraint, I was able to run 10-ns MD simulation for the system at 300k without any problem. However at high temperature (600k), the waters and lipids start to expand in both directions of Z-axis. If I turn on the surfacetension, they would expand in X and Y directions instead. Since NAMD does not allow to have both constant area and surface tension at the same time, I wonder if there is a way to exert forces in X, Y and Z directions to hold the system together.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:54 CST