From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue Dec 05 2006 - 12:19:31 CST
A possible reason why the pressure drops would be if forces from the Tcl
interface were not included in virial calculations. It would be good to have
confirmation from NAMD people on that, since many uses of TclForces could be
About getbond: it just computes the distance between two 3d vectors, it has no
clue what PBCs are. The code of that function essentially reduces to
(r2-r1).length(). So the relevant question is, where do you get the
coordinates you feed to getbond? Presumably loadcoords...
On Friday 01 December 2006 17:53, Arturas Ziemys wrote:
> I have the questions on Tcl Force still.
> I applied the "soft" repulsive force from the center of the water box to
> some water molecules. It was very strange thing to find that the pressure
> dropped significantly (to -80 bars), while I used Langevin Piston targeted
> at 1 bar .
> How that effect could be explained ??
> I could understand that if I would apply the attractive force acting to the
> center of my systems, the pressure could drop. Any comments are welcome !
> P.S. However I still got no answer about the Tcl function 'getbond' and how
> it deals with PBC ... :) ...
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