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

[William Foskett]

Thanks for the help!

For the sake of density distribution, suface tension, and surface potential
analysis I think that these PBC artefacts affect the results.

For example, if I use the g_density function to analyse the carbon
distribution on a box that initially has 5 1-butanol molecules at each
interface, and at the end it has 6 at one and 4 at the other, the density
results show one peak higher than the other, corresponding to the interface
that has 6 molecules rather than 4.

This is proving difficult as the aim of my study is to compare the effect
of the structure of 1-butanol and isobutanol on the surface adsorption of
ions (here, Na+ and Cl-) by analysing the properties mentioned above.
However, I can't get consistent results due to these PBC artefacts.

Thanks,

Billy


On Wed, May 7, 2014 at 7:09 AM, Dallas Warren <Dallas.Warren at monash.edu>wrote:

> PBC artifacts means that what you are observing is a visualisation effect.
>  The molecules are not moving between the interfaces.  It is not something
> you use to do anything, other than to confuse those new to simulations ;-)
>
> In VMD, there is an option in the graphical representation window, check
> under the Periodic tab.  You can turn on periodic images in six different
> directions from your original simulation box.  Have a play with that and it
> will help you to get an idea on how periodic boxes work and how your
> molecules are moving around within them.  If you require your molecule to
> not move around in the manner it has, such as you want to make a movie to
> show others, then there are options to eliminate PBC jumps in the
> trajectory processing script trjconv.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> > William Foskett
> > Sent: Tuesday, 6 May 2014 4:34 PM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Alcohol molecules moving from water/vacuum
> > interface
> >
> > 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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