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 <ericsm...@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.