[gmx-users] SASA calculation for one replica in REMD

[Dallas Warren]

The trajectory output from GROMACS is specific to that specific
ensemble, in your case at given temperature.  So each individual
trajectory is for a given temperature.  And that sounds like it is
exactly what you want.

If you want to follow the trajectory for a single replica, that's when
it gets a little more complicated and you need to use the demux script
and some further processing.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.




On Mon, 29 Apr 2019 at 13:56, Shan Jayasinghe
<shanjayasinghe2011 at gmail.com> wrote:
>
> Dear Gromacs Users,
>
> Thank you for all suggestions. Yes I can use gmx SASA, but I want to know
> how do we use that in REMD simulations?
>
> Specifically, I want to calculate SASA for molecules in my first replica
> (298 K). But I think the trajectory in the first replica contains the
> information regarding to temperature exchanges. However, I want to
> calculate SASA for specifically at 298 K. How can we extract information
> only for 298 K.
>
> Thank you for any help that you can provide.
>
>
>
> On Tue, Apr 23, 2019 at 7:38 PM Tasneem Kausar <tasneemkausar12 at gmail.com>
> wrote:
>
> > Check gmx sasa -h
> > It is implemented in Gromacs
> >
> > On Tue, Apr 23, 2019 at 2:37 PM Shan Jayasinghe <
> > shanjayasinghe2011 at gmail.com> wrote:
> >
> > > Dear Gromacs Users,
> > >
> > > I did replica exchange molecular dynamics simulation which contains 25
> > > replicas. Now I want to calculate the solvent accessible surface area of
> > > the surfactant (the first replica in my REMD) I used in my simulation at
> > > 298 K. How can I do that?
> > >
> > > Can anyone help me?
> > >
> > > Thank you.
> > > --
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> --
> Best Regards
> Shan Jayasinghe
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