[gmx-users] High density after genbox

[Mark Abraham]

The simulation uses the .itp contents, which goes into the .tpr. But in
general the other tools either don't read that part of the .tpr, or you
didn't give it to them in the first place (so they make do with
atommass.dat).

Mark


On Wed, May 21, 2014 at 1:53 PM, sujithkakkat . <sujithks58 at gmail.com>wrote:

> 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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