Thanks Justin for the reply. I did read the help and manual and understand that the output file can be the whole or part of the calculation group. What I don't quite understand is what the output group represents. I am assuming that the calculation group would be the group of atoms that will be probed to determine the solvent accessible are. If so, what does the output group represent?
Thanks. -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Justin A. Lemkul Sent: Thursday, April 23, 2009 6:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_sas Cheong Wee Loong, Daniel wrote: > Dear all, > > > > I am interested to calculate the hydrophobic and hydrophilic area of the > surface of the protein layer I am simulating. It looked like g_sas > would be able to give me what I was looking for. But I was wondering > what the difference is between the calculation group and the output > group. In particular, what is the output group? I tried looking in the > manual and in the archives but I can't seem to find an answer to it. > From g_sas -h: "The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group." -Justin > > > Thanks. > > > ------------------------------------------------------------------------ > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. Please > do not copy or use it for any purpose, or disclose its contents to any > other person. Thank you. > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > 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 -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list [email protected] 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 This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. _______________________________________________ gmx-users mailing list [email protected] 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
