[gmx-users] Related to REMD

Mark Abraham mark.j.abraham at gmail.com
Tue Jan 2 12:22:30 CET 2018


You can't fix all three of temperature range, number of replicas and
transition probability. Shameless self plug:


On Tue, Jan 2, 2018 at 11:44 AM 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
> and also tell how to extract the one seed conformation from multiple seed
> conformation which i had generated using above command.
> Thanks in advance
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