[gmx-users] REMD general protocol ...

[Erik Marklund]

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.
> 
> -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?

Erik

> 
> -- 
> ========================================
> 
> 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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