Dear Amber users,
I have some difficulties with constant pressure MD runs. The system is a solvated molecule inside a box with periodic boundary conditions. After equilibration at 300K with constant volume, I wanted to run at constant pressure. When I choose the default target pressure pres0=1.0 [atm] then the VOLUME of the box slightly shrinks during MD using input
&cntrl
ntc=2, ntf=2, iwrap=1,
cut=10.0, ntb = 2,
ntpr=50, ntwx=50,
nstlim = 1000, dt=0.002,
ntt=1, temp0=300.0, tautp=1.0,
ntp=1, pres0=1.0, taup=0.2,
ntx=5, irest=1, nscm=100
&end
The PRESS variable in output file starts correspondingly negative (-654.0), and converges to zero. However, when I choose pres0=0.0 for gas phase, the box still shrinks although less strongly. I would have expected that the system would expand at zero applied pressure at 300K (?) I also tried a negative target pressure pres0 which surprisingly didn't give an error message and still led to a slight shrinking of the box. Does anyone understand how the pressure control works (in particular at low pressures)?
Many thanks,
Robert
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Received on Wed Jan 14 2004 - 15:53:13 PST