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

Dallas Warren Dallas.Warren at monash.edu
Wed May 7 04:09:47 CEST 2014


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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