[gmx-users] g_sas

rajat desikan rajatdesikan at gmail.com
Sat Aug 16 17:45:39 CEST 2014

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


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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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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