[gmx-users] REMD general protocol ...
erikm at xray.bmc.uu.se
Tue Apr 2 13:38:53 CEST 2013
On 2 Apr 2013, at 13:30, Justin Lemkul <jalemkul at 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.
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?
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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