Open GoogleCodeExporter opened 8 years ago
Hi
After looking into post update scripts for pressure correction, I found out
that we dont have to do much to enable pressure correction with relative
entropy and we can use (almost) the same post_update scripts for relative
entropy. Only thing, that is needed to take care is that instead of adding
correction to .dpot, the correction should be added to .pot.new, the potential
file written by csg_reupdate.
Now, I am a bit confused about how the pressure correction is done in the case
of mixtures. For mixtures, user would specify how much each interaction should
contribute to the total pressure of a system, i.e., the target pressure for an
interaction. Then votca should determine the actual pressure contribution of
each specific interaction and add corresponding correction based on error in
each case.
However, from the script, I understand that gromacs' g_energy is used to
compute CG pressure from current CG-MD simulations. Then this pressure is used
to determine the difference between user specified target pressure. However,
g_energy is computing the total pressure and not the contribution from a
specified CG interaction. Therefore, in the case of mixture, wouldnt it cause
excessive correction (multiple counting of error) in each interaction?
I think, one solution to this issue would be to specify pressure correction
frequency for each interaction such that only one interaction is corrected at
any given iteration. Am I correct? Am I just re-iterating what you guys have
already thought about :)
Thanks
Sikandar
Original comment by symasha...@gmail.com
on 13 Nov 2013 at 5:29
Well, yes, for multi-component systems, one would need to calculate the partial
pressures. Espresso is able to do that, but Gromacs isn't. We always had the
plan to add this feature to Gromacs, but as pressure correction got less and
less popular with the years, so it never happened. (We should add a warning to
csg_inverse though!)
Considering that all components contribute equally according to the number of
pairs, one can calculate an estimate for the partial pressures. Technically the
ratio, N_pairs_XY/N_pairs_total can then be used as the scale of the pressure
correction. However, this approximation is pretty crude.
Original comment by christop...@gmail.com
on 13 Nov 2013 at 5:56
one more option to get partial pressures from gromacs would be to do mdrun
-rerun with energy exclusion group. With this option one can exclude all
interactions except for a given pair of particles and then the pressure
from g_energy will have virial component due to interaction of interest.
Original comment by symasha...@gmail.com
on 13 Nov 2013 at 6:14
Original issue reported on code.google.com by
symasha...@gmail.com
on 12 Nov 2013 at 7:12