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

Wed May 7 14:14:08 CEST 2014

So theoretically if I removed the NPT run I shouldnt see this movement?
On 07/05/2014 8:07 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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!
>>>>>> --
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> --
> ==================================================
>
> 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
>
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