Dear Amber users,
I am trying to compute the surface tension of a solution that is run, in
amber, in a slab configuration. The formula for the surface tension,
gamma, that I want to use is the following:
gamma=(Lz/2)(Pzz-0.5(Pxx+Pyy))
To obtain the pressure components I run the system in a "fake" NPT, i.e.:
set ntb=2, ntp=1, and taup=999999 (as also David Case suggested:
http://amber.ch.ic.ac.uk/archive/200506/0048.html).
Now because my simulations are in a slab configuration (i.e., the
computing box is elongated in the z direction and vacuum is present
between "wafer" of liquid) the pressure I get in the mden file is negative
since if the system could (if it were really run at constant pressure) it
would contract and eliminate the vacuum (as David Case very clearly states
in
http://amber.scripps.edu/Questions/pressure.html).
OK, here are my questions:
1) is that right that if my system had air (say a mixture of N2 and O2 to
obtain the correct atmospheric pressure) in place of the vacuum I would
not get a negative pressure?
2) if the previous is true and I still do not have air to stabilize the
pressure on the slab are the components of the pressure meaningful and can
I still use them to compute the surface tension with the formula given
above?
Any help would be deeply appreciated!!!
Thanks,
Raffaella.
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Received on Wed May 02 2007 - 06:07:23 PDT
