[gmx-users] High density after genbox

[sujithkakkat .]

Thank you Mark,

 My Bad.   Now fixed.

 Hope the simulations I did before were not affected, I had defined
atomtypes with the correct mass in the .itp file used.

Sujith


On Wed, May 21, 2014 at 12:59 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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?
>
> Mark
>
>
> 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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