Re: how to get the energy in vacuum of a molecule in NAMD

From: Jim Phillips (
Date: Wed Jul 20 2011 - 11:25:59 CDT

That will work, assuming you also adjust the switching and pairlist
distances to be something like 990 and 1100. In the current 2.8 release
this will give you one big patch that won't scale beyond a single core.
I just put in some changes, available in the nightly build version, that
will scale better, although if you're just evaluating enery once you're
not going to get much benefit from measurement-based load balancing
(implicit solvent will likely benefit, though).

Bear in mind that your forcefield was designed for a specific solvent
model and cutoff distance so vacuum energies aren't that meaningful.


On Wed, 22 Jun 2011, jnsong wrote:

> Dear all,
> I want to get energy of a structure in vacuum using NAMD. But I have no
> idea how to do this in NAMD. In AMBER, one just set the threshold of
> cutoff to be 999 and without box, the method has described in the
> tutorial of AMBER. But to NAMD, I haven't found any method to obtain
> this energy like in AMBER. So I come here seeking some help.
> Thanks in advance!
> Sincerely,
> Jianing
> --
> Jianing Song
> Ph. D. Student
> Institute of Theoretical and Computational Sciences
> Dept. Phys.
> East China Normal University
> 200062
> 3663 North Zhongshan Road
> Shanghai, P. R. China

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