Re: Accelerated MD: question about dual boost mode

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue May 10 2011 - 10:17:59 CDT

Sorry for being so unspecific.
I meant by calculating it from the DCD if one does not have the output file.
For the outputfiel I wrote my own little python script which is a bit more
flexible then NAMDplot (For example it can glob multiple consecutive output
files)
http://olausson.de/scriptarchive/16-modeling/56-anamopy
http://olausson.de/downloads/view.download/6-modeling/16-anamopy

But after searching around I realized that I can calculate it quickly with the
NAMD Plug-In "NAMDEnergy" - sweet, this saved me some time for firing up
CHARMM with a custom script, to just get a clue.

Thanks,
Bjoern

On Tuesday 10 May 2011 15:36:35 patrick wintrode wrote:
> You can get a decent visual estimate just using namdplot. That gets you in
> the right ballpark, but it's not quantitative.
>
> Patrick L. Wintrode
> Assistant Professor, Dept. of Physiology & Biophysics
> Case Western Reserve University
> Cleveland, OH 44106
>
> --- On Tue, 5/10/11, Bjoern Olausson <namdlist_at_googlemail.com> wrote:
>
> From: Bjoern Olausson <namdlist_at_googlemail.com>
> Subject: Re: namd-l: Accelerated MD: question about dual boost mode
> To: "Jeff Wereszczynski" <jmweresz_at_mccammon.ucsd.edu>
> Cc: "patrick wintrode" <pat_wde2_at_yahoo.com>, namd-l_at_ks.uiuc.edu
> Date: Tuesday, May 10, 2011, 7:32 AM
>
> 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:54 CST