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

Wed May 7 14:06:15 CEST 2014

On 5/7/14, 12:38 AM, William Foskett wrote:
> 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.
>

The only way you can do this is with NVT.  When running NPT, the vacuum space 
you left collapses, hence you no longer have interfaces, just a continuous 
system via PBC, hence molecules jump back and forth.

-Justin

> 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!
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>> or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================