[gmx-users] g_sas

[Eric Smoll]

Rajat,

Thank you for the rapid response. It is very helpful.

"1) Yes. Use a probe radius of 0 nm.
2) No. There is no verbose option in g_sas AFAIK. As an aside, you may want
to reconsider -xvg none
3) No difference in my experience."

Let me get this straight. You are saying that analyzing a .trr outputs an
average, not trajectory-like information. You are saying, for your specific
system, you see little difference in the surface formed from analyzing a
trajectory and analyzing a snapshot. That may be for a protein but I am
studying a molecular liquid.

"4) g_sas uses vdwradii.dat, which may not have the vdw radius for a
particular atom type. Eg: Phosphorus is not present by default in
vdwradii.dat (for phosphorylated proteins). You may add this manually to a
local copy of vdwradii.dat"

Thank you. Exactly, the information I was looking for!

"Sorry, I misread your mail. You cannot compute the vacuum accessible
surface area for a liquid because the molecules are in constant motion."

So are you saying that *I cannot use g_sas to compute the vacuum accessible
surface area for a liquid at all* or *I cannot use g_sas to compute the
vacuum accessible surface area with a trajectory*?

Surely we can define a vacuum accessible surface for any timestep of this
trajectory, correct? I agree that molecules at the surface are constantly
changing making the definition of a surface ill-defined over a trajectory
but I am looking for some way to obtain a time-averaged atom-composition of
the liquid surface. If g_sas can be used for temporal snaphot .gro file,
perhaps I can extract a variety of timesteps and carry out the calculation
manually.

Thanks again Rajat,

Best,
Eric


> Message: 7
> Date: Sat, 16 Aug 2014 21:17:36 +0530
> From: rajat desikan <rajatdesikan at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] g_sas
> Message-ID:
>         <
> CA+d_LwtqQ+0GPhTQ+8WQhoLrfQbwY6Ycz6Q-i4YAg7HwmzHe-A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Eric,
> Sorry, I misread your mail. You cannot compute the vacuum accessible
> surface area for a liquid because the molecules are in constant motion.
>
> Regards,
>
>
> On Sat, Aug 16, 2014 at 9:15 PM, rajat desikan <rajatdesikan at gmail.com>
> wrote:
>
> > Hi Eric,
> > 1) Yes. Use a probe radius of 0 nm.
> > 2) No. There is no verbose option in g_sas AFAIK. As an aside, you may
> > want to reconsider -xvg none
> > 3) No difference in my experience.
> > 4) g_sas uses vdwradii.dat, which may not have the vdw radius for a
> > particular atom type. Eg: Phosphorus is not present by default in
> > vdwradii.dat (for phosphorylated proteins). You may add this manually to
> a
> > local copy of vdwradii.dat
> >
> > Regards,
> >
> >
> > On Sat, Aug 16, 2014 at 9:01 PM, Eric Smoll <ericsmoll at gmail.com> wrote:
> >
> >> Hello,
> >>
> >> I am interested in using g_sas in gromacs 4.6.5. I have a few questions:
> >>
> >> 1.) Is it advisable to use this tool to compute the vacuum accessible
> >> surface area for a liquid?
> >>
> >> 2.) I ran a test using .gro / .trr / .tpr output from a production run
> in
> >> my workflow as shown follows: { g_sas -f A.gro -s A.tpr -o TEST1.xvg
> -xvg
> >> none -b 2000 -e 4000 -probe 0.15 -pbc -minarea 0.2 -ndots 24 -i
> TEST1.itp;
> >> g_sas -f A.trr -s A.tpr -o TEST2.xvg -xvg none -b 2000 -e 4000 -probe
> 0.15
> >> -pbc -minarea 0.2 -ndots 24 -i TEST2.itp }. The .trr / .tpr run produces
> >> no
> >> output while processing so it is unclear when it will end. Is there
> anyway
> >> to enable output that will report on the progress of the calculation?
> >>
> >> 3.) What are the difference in output when processing a .gro vs a .trr?
> >> Does trajectory input produce trajectory output or some sort of average?
> >>
> >> 4.) When running on the .gro / .tpr combination I received the following
> >> error:
> >>
> >> WARNING: Masses and atomic (Van der Waals) radii will be guessed
> >>          based on residue and atom names, since they could not be
> >>          definitively assigned from the information in your input
> >>          files. These guessed numbers might deviate from the mass
> >>          and radius of the atom type. Please check the output
> >>          files if necessary.
> >>
> >> WARNING: could not find a Van der Waals radius for 640 atoms
> >> 29440 out of 34560 atoms were classified as hydrophobic
> >>
> >> Note that I am using 640 molecules in my liquid simulation. I have not
> >> received this error for any other step in my molecular dynamics
> workflow.
> >> It concerns me. Is this an indication that my coordinate and parameter
> >> files are somehow incomplete? How do I go about troubleshooting this and
> >> specifying the missing parameters?
> >>
> >> Best,
> >> Eric
> >> --
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> >>
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> >
> >
> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> >
>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
>