VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Sat Aug 30 2003 - 19:30:56 CDT

Hi,

This doesn't seem to be available in NAMD 2.5b1. Ask Jim to send you
a more recent version; the documentation included with 2.5b2 should
also have information on how to use the pair interaction features.

Thanks,
Justin

On Fri, Aug 29, 2003 at 09:24:44PM -0700, Ioana Cozmuta wrote:
> 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
> >
> > 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys