[gmx-users] reg electrostatic potential

Justin A. Lemkul jalemkul at vt.edu
Sun Jul 3 14:09:20 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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