Re: Accelerated MD: question about dual boost mode

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue May 10 2011 - 07:32:13 CDT

On Friday 01 April 2011 00:07:07 Jeff Wereszczynski wrote:
> [...]
> Run a
> short classical MD simulation and calculate the average dihedral potential
> energy (V_d) and the average total potential energy (V_tot). For a system
> with Nres residues and Natom atoms, a good starting point for the dihedral
> parameters may be:
>
> E_dihed=V_d+4*Nres
> alpha_dihed=4*Nres/5
>
> And for the total you could try:
>
> E_tot=V_tot+N_atom/5
> alpha_tot= N_atom/5
>
> [...]
>

Hi,

i just wanted to know if there is some script or existing plug-in for VMD to
calculate average dihedral potential and average total potential energy before
I try to hack one together on my own :-(

Cheers,
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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