Re: [gmx-users] g_sas for martini coarse-grained particles
the vdW radius of Martini particues is 0.263 nm, or 0.526 nm for the diameter. This is clearly indicated in all the martini papers :)) On Jul 18, 2010, at 1:59 AM, Sanku M wrote: Hi, I am trying to estimate the solvent accessible surface area of hydrophobic tails of a martini DPPC lipid bilayer . I was going to use g_sas for that. But, I observe that this tool gets the vanderwal radii from vdwradii.dat file. But, since the particles in the martini lipids are united-atom types, I was wondering what will be a reasonable radius to use for hydrophobic tail particles of a martini lipid ? Thanks Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_sas for martini coarse-grained particles
also an example of the use of SASA is in JACS-2007, 129, 10126-10132 On Jul 18, 2010, at 1:59 AM, Sanku M wrote: Hi, I am trying to estimate the solvent accessible surface area of hydrophobic tails of a martini DPPC lipid bilayer . I was going to use g_sas for that. But, I observe that this tool gets the vanderwal radii from vdwradii.dat file. But, since the particles in the martini lipids are united-atom types, I was wondering what will be a reasonable radius to use for hydrophobic tail particles of a martini lipid ? Thanks Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sas for martini coarse-grained particles
Hi, I am trying to estimate the solvent accessible surface area of hydrophobic tails of a martini DPPC lipid bilayer . I was going to use g_sas for that. But, I observe that this tool gets the vanderwal radii from vdwradii.dat file. But, since the particles in the martini lipids are united-atom types, I was wondering what will be a reasonable radius to use for hydrophobic tail particles of a martini lipid ? Thanks Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
