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

[Mark Abraham]

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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