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 <rajatdesi...@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 <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 > -- 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.