Re: Defining a group of atoms in a simulation

From: Ilja Khavrutskii (ikhavru_at_mccammon.ucsd.edu)
Date: Sat Jan 19 2008 - 14:02:58 CST

Hi,

To restrain a group of atoms NAMD has the following functionality (that
does not require TCL scripting).

freeEnergy on
freeEnergyConfig {
urestraint {
  posi group { (ADPR,381) } kf=10 ref=(14.426 8.281 -3.596)
}
pmf {
     task = stop
     time = 1 ps
   }
}

for example. It does work (tested it myself).

However, I would like something more general, i.e. to be able to specify
kf for x, y and z separately. This way I would be able to restrain the
group's COM z-direction only for example. I would really appreciate if
some of the developers took time to implement this simple extra feature.

This should be simple enough, and on the user's end it should look like:
posi group { (ADPR,381) } kf=(0,0,10) ref=(14.426 8.281 -3.596)}

That would be my wish. Could you please add it to the wish list?

Otherwise, one has to go into TCL as a number of people have suggested and
implement the same thing on that level.

If somebody already has a TCL script for COM say z-direction only
restraint, could you please share? I need one that would work properly
with the NPT.

Best,
-Ilja

On Sat, 19 Jan 2008, Arneh Babakhani wrote:

> Hi,
>
> I was wondering, is there a way in NAMD to define a group of atoms, and
> then perform some action on the center-of-mass of said group? (such as
> pulling, constraining, etc).
>
> I was unable to find any such direction in the manual, and this question
> has been posted before, for instance here:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1807.html
> but with no definitive answer (as far as I know).
>
> If you could point me in the right direction, would greatly appreciate it,
>
> Thanks,
>
> Arneh
>

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