[gmx-users] Related to REMD

[ISHRAT JAHAN]

Thank you Sudip


On Thu, Jan 4, 2018 at 2:50 PM, Sudip Das <das.sudip37 at gmail.com> wrote:

> Hi Ishrat,
>
> As per REMD, you are supposed to generate different .tpr files for
> different replicas at their corresponding temperature and simulate
> simultaneously all the replicas. As for example, if you are having 5
> replicas,
>
> replica:  0       1         2        3        4
> temp:    300    305    312    322    335
>
> Have a look into GROMACS REMD tutorial.
>
> Regards,
> Sudip
>
> ‌
>
> Sudip Das
>
> PhD Student
> C/o. Prof. S. Balasubramanian
> Molecular Simulations Lab
> Chemistry and Physics of Materials Unit (CPMU)
> Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
> Bangalore, India
>
> On Thu, Jan 4, 2018 at 12:20 PM, ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
>
> > Hi Sudip
> > For doing REMD,I have generated the five seed conformation using trjconv
> > command. I have taken only 10 temperature from the temperature generating
> > tool, now i want to know whether i have to generate different .tpr file
> > using one conformation at all temperature or all conformations at all
> > temperature. Will you please tell me what to do as i am unable to
> > understand?
> > Thanks in advance
> >
> >
> > 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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