From: Chris Harrison (charris5_at_gmail.com)
Date: Fri Nov 04 2011 - 19:01:07 CDT
I need to briefly clarify: the V of the replicas should be approximately
equivalent. The T varies, as dictated by each given replica.
On Friday, November 4, 2011, Chris Harrison <charris5_at_gmail.com> wrote:
> Temperature based REMD requires an NVT ensemble, which imposes a constant
volume. Just make sure you're running in an NVT ensemble as per your NAMD
configuration, ie, constant temp and volume.
> On Friday, November 4, 2011, Jiao, Dian NMN (-EXP) <dnjiao_at_sandia.gov>
>> 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>
>> Date: Fri, 4 Nov 2011 17:56:12 -0400
>> To: Dian Jiao <dnjiao_at_sandia.gov>
>> Cc: "namd-l_at_ks.uiuc.edu" <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>
>>> 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.
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> char_at_ks.uiuc.edu Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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