[gmx-users] pressure with amber ff

[Michel Cuendet]

Hi everyone,

  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 
does)
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 
equilibration :

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 ?

  Have fun,

Michel