On 4/2/13 7:38 AM, Erik Marklund wrote:
On 2 Apr 2013, at 13:30, Justin Lemkul <jalem...@vt.edu> wrote:
On 4/2/13 7:13 AM, rama david wrote:
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I thoroughly search the Mailing-list Archive for the REMD problem.
It was a really helpful to start.
My system consist of peptide + water.
I used the following work-flow, Would you please help me to find out
my mistakes...
1. energy minimesation for peptide + solvent
2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
3. Make tpr file for each nvt run
4. Then separate equilibration for each temp ( 4 equilibration steps )
5. Then made NPT.mdp file for each temp ( 4 temp )
6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps )
7. Then run md production with -replex 1000 -multi 4 command ..
To determine the temp I used web-server http://folding.bmc.uu.se/remd/
Please suggest me any improvements that are possible to implement in
my work flow.
Such a narrow range of temperatures defeats the purpose of using REMD.
Normally, a much larger range is used over many more simulations. For
near-ambient temperatures, NPT can be used, but if you include much higher
temperatures, you should use NVT due to box instability upon exchanges.
-Justin
Sure, the enhanced sampling is basically gone, but you can deduce temperature
dependences from such simulations and to some extent benefit from the mixing,
can't you?
I suppose, but then why bother with the exchange overhead? Seems to me that if
you're only interested in temperature-dependent quantities, you can do that with
independent simulations at different temperatures.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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