VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Jun 12 2003 - 11:32:45 CDT

Hi,

Excellent observation. The reason for this is that NAMD's conjugate
gradient minimizer uses the reported energies as the primary criteria and
only uses forces to accelerate convergence. Since IMD only adds forces to
the simulation without any energy component, it doesn't affect
minimization in the same way as dynamics. This is fixable, and we'll need
to look into it further. In the meantime, the "velocityQuenching on"
option can be specified during normal dynamics to give a very crude
minimizer that would respond to IMD forces.

Sorry for the confusion, and thanks for pointing this out.

-Jim

On Thu, 12 Jun 2003, Marc Baaden wrote:

>
> Hi,
>
> dan_at_chalkie.org.uk said:
> >> I wish to perform interactive molecular dynamics, actually interactive
> >> energy minimisation using namd2 with VMD
>
> I might be mistaken, but as far as my tests went,
> NAMD "only" does interactive MOLECULAR DYNAMICS but
> no minimization. I think you *do* visualize the
> minimization, but eg application of forces is not
> taken into account.
>
> Please correct me, if I am wrong,
>
> Cheers,
> Marc Baaden
>
> --
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden_at_smplinux.de - http://www.marc-baaden.de
> FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217
>
>