From: Fangqiang Zhu (fzhu_at_ks.uiuc.edu)
Date: Tue Dec 02 2003 - 00:04:16 CST
I think in the current version of NAMD, "fixedAtomsForces on" is not required
for constant pressure simulations, at least this is not enforced by the program.
my opinion, those forces shouldn't be included in the pressure calculation at
However, one should be aware that when a large fraction of the atoms are fixed,
the pressure calculation will be somewhat inaccurate. But, in my opinion, this
problem can't be solved at all by including forces between fixed atoms.
things can even be worse if those forces are included. In practice, at early
equilibrium stage, I often need to fix some atoms and run constant pressure
simulations, with forces on fixed atoms ignored, and everything seems fine. So
I disagree with the instruction in the NAMD manual regarding the
Again, this is my personal opinion, and Jim may have different views...
Jan Saam wrote:
> Hi all,
> When you are trying to simulate a system using constant pressure then NAMD
> requires that all forces, including the ones between fixed atoms are
> calculated ("fixedAtomsForces on").
> I assume this is somehow due to the the pressure calculation scheme that uses
> the atomic virial and kinetic energy.
> But couldn't one just take omly the moving atoms into account?
> I remember that "fixedAtomsForces on" was not required in former versions of
> NAMD. How did it work then?
> Does anybody know about this?
> Jan Saam
> Institut für Biochemie
> Monbijoustr. 2
> 10117 Berlin
> 030-450 528 449
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