[gmx-users] pressure with amber ff
michel.cuendet at epfl.ch
Tue Apr 27 15:53:00 CEST 2004
I submitted a while ago this problem to the list : In a noncubic box,
you get highly negative pressures with the amber ff. My test system is a
dipeptide in a 6.3:3.2:3.0 nm box. I discovered that the problem relies
on the masses of the water atoms, together with the SETTLE algorithm.
Masses amber O : 16.00000 H : 1.00800 (like ambconv
Masses Periodic Table 0 : 15.99940 H : 1.00794
Masses spc O : 15.99940 H : 1.00800
I got the following results for average pressure [bar] after
tip3p, masses amber : -500
tip3p, masses PT: +1500
tip3p, masses amber, no SETTLE : ~1
spc from gmx : ~1
tip3p with spc mass : ~1 -> OK
This means that the conversion only works when using the spc masses.
Ambconv has to be updated.
This only cures the symptoms... Why is the virial calculation in
SETTLE so much dependent on the masses ?
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