Re: membrane simulation at high Temp

From: Jiao, Dian NMN (-EXP) (
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 <<>>
Date: Fri, 4 Nov 2011 17:56:12 -0400
To: Dian Jiao <<>>
Cc: "<>" <<>>
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) <<>> wrote:
Hi all,

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.


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