[gmx-users] g_sas

[rajat desikan]

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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>
>
>
> --
> 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