[gmx-users] REMD general protocol ...
ramadavidgroup at gmail.com
Tue Apr 2 13:13:17 CEST 2013
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
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,
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