[gmx-users] Related to REMD

[ISHRAT JAHAN]

My system contains only 95 protein atom and 750 sol molecule.

On Tue, Jan 2, 2018 at 4:55 PM, Sudip Das <das.sudip37 at gmail.com> wrote:

> 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
>
>
> Regards,
> Sudip
>
>
> Thanks in advance
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