[gmx-users] Related to REMD

Sudip Das das.sudip37 at gmail.com
Tue Jan 2 12:25:21 CET 2018

Hi Ishrat,

On Tue, Jan 2, 2018 at 4:14 PM, ISHRAT JAHAN <jishrat17 at gmail.com> wrote:

> Dear all,
> I am trying to do REMD simulation. I had equillbrated the system for 5ns
> and extracted the seed conformation at 3ns using the command-
> gmx trjconv -f traj.trr -o 3ns.gro -s topol.tpr -dump 3000 -pbc mol
> I had used temperature generator for REMD simulation from
> folding.bmc.uu.se/remd with transition probability of 0.25 in temperature
> range of 290-400K.it gives too many replica and i want only 10 replica.

will anyone tell me what criteria should be taken for taking 10 replicas

It seems that your system size is reasonably large. You can try using
replica exchange with solute scaling (REST2 method) which is basically
comes under Hamiltonian replica exchange. It will reduce the number of
replicas by scaling the potential energy surface with respect to effective
temperature of the corresponding replica.

> and also tell how to extract the one seed conformation from multiple seed
> conformation which i had generated using above command.

See the several options under the module trjconv by typing the command:
gmx trjconv -h


Thanks in advance
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