[gmx-users] Related to REMD

[Mark Abraham]

Hi,

You can't fix all three of temperature range, number of replicas and
transition probability. Shameless self plug:
http://pubs.acs.org/doi/abs/10.1021/ct800016r

Mark

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>