[gmx-users] SASA Problem (Mark Abraham)

[Tom]

Hi Mark,

It should give the value of the area of two faces instead of the a single
face area, right?

I am testing a gold surface with 1-nm thickness. Gold surface has pbc
bonded in both
directions
g_sas converges to the value around two-face area.

Graphene surface converges to one surface area. For this grapheme surface,
one dimension has PBC bonded with the image atom.

BTW:
For a plane surface, the result very sensitive to the option of -ndots. The
results only converge
when ndots value is very large. For a protein, it is not sensitive.
Thanks for any advice!

I will check the source code also.

Tom

>
> Message: 5
> Date: Tue, 17 Nov 2015 20:01:29 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] SASA Problem
> Message-ID:
>         <
> CAMNuMATenu8FTwhrZqE9eLakKcodGVcXZOF-dV62G_5W+a-q8g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Does all of the output of gmx sasa agree with what you think should be
> going on?
>
> Mark
>
> On Tue, Nov 17, 2015 at 5:28 PM Tom <dnaafm at gmail.com> wrote:
>
> > Dear All,
> >
> > I am calculating SASA of a grahene surface which is PBC bonded with image
> > atoms.
> > My system has a graphene soaked with water in one phase.
> >
> > My surface is around 5*10 nm^2.
> > Why SASA give the value close to single face area?
> > I adjusted ndots until SASA converged to 72 nm.
> >
> > I copied the VDW radii in the current directory and made sure that it has
> > the parameter for
> > graphene atoms.
> >
> > Thanks for the help!
> >
> > Tom
> > --
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