[gmx-users] High density after genbox

sujithkakkat . sujithks58 at gmail.com
Tue May 20 12:50:36 CEST 2014


    I am working on a water-methane system with OPLSAA for methane and
TIP4P/Ice for water.
What I find strange is that after solvating the methane molecule with water
(tip4p/ice) using the genbox routine, the density appears to be very high
at 1661.04 (g/l) . The number of water molecules is normal for the box
size, and therefore should give lower density values.  After equilibration
steps the density gets back to normal.

    Earlier , I ignored this problem and went ahead with the simulations,
and the end results were found to be good. For eg, the solvation free
energy of methane I calculated , was very close to reported values and also
the value obtained in Justin's tutorial. Another test was simulating the
tip4p/ice water , which gave results, for example the RDFs very close to
the reported results.

   Could some one comment what is going on that gives the high density?



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