[gmx-users] REMD general protocol ...

[Justin Lemkul]

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

-- 
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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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