[gmx-users] Re: rvdw and rcoulomb seem irrelevent in the pull code

[Kun-Lin Yang]

Hi Justin:

        I used the constraint mode (runtype= Constraint).  The system I am
studying is a decanol molecule immersed in a box full of water molecules.  I
want to constraint the decanol molecule and calculate the constraint force.
I think the water structure surrouding the decanol would be affected by the
cut-off radius and eventually the constraint force will also be affected.
However, I changed the cutoff from 0.1 to 1.0 nm for both rcoulomb and rvdw
and the constraint force remain the same.  Please correct me if I am wrong.
Thank you!

Kun-Lin, 2/10


>
> Hi Kun-Lin,
>
> I'm not sure how this is possible. The pull code has absolutely nothing
> to do with the cutoffs. What mode were you using? Ie. umbrella sampling,
> afm, etc... This seems very puzzling.
>
> Justin
>
> > Hi everyone:
> >
> >         I just encoutered something I though very weird.  It seemed to =
> > me the cut-off radius for both van der Waals and Coulombic interations =
> > are irrelevent when I used the pull code.  In other words, no matter =
> > what values I assigned to rvdw and rcoulomb, the output file (pull.pdo)
=
> > seemed identical.  Only the rlist (cut-off radius for the neighbor =
> > searching) is useful.  I'd very appreciate if you have any comments =
> > about this issue.  Thank you!
> >
> > Kun-Lin, 2/9
>
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