Please disregard; I made a typo when selecting my index groups. Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
> > Hi all, > > I recently completed several simulations of pure DPPC bilayers (128 lipids, > 64 > per leaflet, from Tieleman's site), and am processing the output. Of > interest > to me is the SASA, so I'm using g_sas. I ran the command: > > g_sas -f md_0_100.xtc -s md.tpr -n sas.ndx > > (selecting solvent for the calculation, and a subset of my lipids for output) > > I get the following message: > > 0 out of 3200 atoms were classified as hydrophobic > > But yet, if I let the calculation go anyway, I get seemingly reasonable > values > for hydrophobic, hydrophilic, and total SASA. It is odd to me that in a > membrane, none of the atoms are considered hydrophobic. > > Should I be concerned about my results being incorrect, or is it simply > because > the atom types of the acyl chains are unrecognized as standard by g_sas? I > have learned not to ignore such strange messages :-) > > Thanks in advance. > > -Justin > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
