[gmx-users] High density after genbox

Mark Abraham mark.j.abraham at gmail.com
Tue May 20 21:29:17 CEST 2014

Probably "garbage in, garbage out." However you're measuring the density
probably depends on share/top/atommass.dat, which relies on matching atom
names to infer atom types and thus masses. If your atom names don't follow
its assumptions... at least some tools warn about this in the output. Did
the tool you were using not do so?


On Tue, May 20, 2014 at 12:50 PM, sujithkakkat . <sujithks58 at gmail.com>wrote:

> Hello,
>     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?
> Regards,
> Sujith.
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