[gmx-users] Query on generate velocities and gen_temp in mdp files for REMD simulations

[Neha Gandhi]

Dear Help,

I am trying to run REMD simulations and found couple of interesting
discussions on GROMACS mailing list regarding ensembles which can be used
during REMD.

I will be running REMD of small peptide in explicit solvent and I am
confused about gen_temp and gen_vel parameters for these simulations below:

1. NPT ensemble at 310 K to get density right. What should be the
parameters gen_vel and gen_temp set to?
2. Equilibration at each temperature -NVT ensemble. Although equilibration
run will be carried out for a reference temperature range, should the
gen_temp still be set to 310K?
3. Replica exchange -What should be gen_temp and gen_velocity set to?

Many thanks,
Neha


-- 
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
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