VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Aug 29 2003 - 23:24:44 CDT

Hi,

I am using version 2.5b1 that seems to be the latest for download from the
NAMD web page, also the latest manual seems to be for the same version. I
found that variable in the code but I could not find out the way to use it
and print out the information I need.
I would appreciate if you could help me with more details/information.

Thank you very much,
Ioana

PS. Is there somewhere an example available?

On Fri, 29 Aug 2003, Justin Gullingsrud wrote:

> Hi,
>
> This can be done with the pairInteraction set of options in NAMD 2.5b2
> and newer (maybe even newer). Check the User's Guide for details.
>
> Justin
>
> On Thursday, August 28, 2003, at 01:04 PM, Ioana Cozmuta wrote:
>
> > Hi,
> >
> > I have an ion inside a protein and a solvent bath and I want to get:
> > 1. the total force on the ion originating from the protein and
> > separately from
> > the solvent
> > 2. The component of the forces along the z axis
> > 3. The direction of the force from the protein and the solvent ( I
> > want to
> > see where the forces are pointing to)
> >
> > I was thinking to do a single point calculation for different frames
> > in my
> > trajectory but I do not know how to extract the matrix with the vector
> > components of the force.
> >
> > Any suggestion/help would be welcomed!
> >
> > THanks a lot in advance,
> > Ioana
>
>