vidhya sankar wrote:
Dear justin
Thank you for your previous reply.
I would like to calculate absolute and cumulative value
of electrostatic potential at specific distance from surfaces of
particular group of my protein but g_potential calculates only across box
Can't you do this by analyzing each axis separately? If you center the protein
in the box, it should give you some sort of useful information. Otherwise maybe
try the -spherical option. I don't know if it will do what you want, but it
sounds close.
also i would like to calculate vibrational entropy which tool is useful
Maybe g_anaeig (which also means running g_covar first).
further i want to calculate mechanical stiffness of protein .is there is
any tool in gromacs to find out stiffness
Not likely. You can determine flexibility of residues with g_rmsf, but not
mechanical stiffness. Without some applied deformation, I don't know how you'd
quantify this.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
