[gmx-users] g_sas

[Eric Smoll]

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