[gmx-users] REMD general protocol ...

rama david ramadavidgroup at gmail.com
Tue Apr 2 13:13:17 CEST 2013

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.

I will be very grateful to you for your help and suggestion.

With Best Regards,
Rama David

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