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

[Shan Jayasinghe]

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