[gmx-users] Alcohol molecules moving from water/vacuum interface

[William Foskett]

I have inspected the trajectory with VMD 1.9.1. It appears that between two
frames the alcohol molecules jump from one interface to the other - rather
than diffusing through the bulk over time.

I had not considered PBC artefacts - I am fairly new to these molecular
simulations. I have just read into PBC artefacts and it seems that this
could be a possible solution to the problem. Could these used to limit the
area in which the alcohols molecules could move?




On Tue, May 6, 2014 at 2:21 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Have you inspected the trajectory? Are you seeing PBC artifacts?
> On May 6, 2014 7:52 AM, "William Foskett" <whfoskett at gmail.com> wrote:
>
> > Hello,
> >
> > I am completing simulations of 1-butanol and isobutanol molecules at a
> > vacuum/water interface for a bachelor final year research project. I have
> > set up a box of molecules with two vacuum/water interfaces (at either end
> > of the box on the xy plane) the following commands (example of 5
> isobutanol
> > molecules per interface in a 3 x 3 x 10 box)
> >
> > *genbox -ci isobutanol.gro -nmol 5  -box 3 3 1 -o layer.gro -p topol.top*
> >
> > *editconf -f layer.gro -o layer2.g96 -box 3 3 2 -center 1.5 1.5 1*
> >
> >
> > *genconf -f layer2.g96 -o 2layers.gro -nbox 1 1 2 -dist 0 0 6*
> >
> >
> > genbox -cp 2layers.gro -cs spc216.gro -o box1.g96 -p topol.top -box 3 3
> 10
> >
> >
> > And then proceeded to run energy minimisation,a 20ps NVT run, a 40ps NPT
> > and finally a 20ns NVT run following compacting of the box based on a
> > *gmxcheck
> > -c NPT_40ps.g96 *
> >
> >
> > The problem I am having is that alcohol molecules continually jump
> between
> > the interfaces. For examples, if I started with 5 molecules at one
> > interface and 5 at the other, I may end up with 6 and 4 at the end of the
> > series of simulations. This generally occurs in the NVT or NPT runs. The
> > isobutanol molecules seem to behave appropriately as surfactants, and
> > therefore I cannot isolate why they are moving between interfaces.
> >
> >
> > Is there any way that I can force the molecules to maintain their
> original
> > equal split without molecules jumping between interfaces?
> >
> >
> > If you require more information please let me know.
> >
> >
> > Thank you!
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