[gmx-users] NPT equilibration without pbc

[Rajorshi Paul]

Thanks Alex for the suggestion!!

On 5 March 2017 at 01:49, Alex <nedomacho at gmail.com> wrote:

> I looked at that paper and there are no attempts to simulate liquid-gas
> equilibrium at normal atmospheric pressure. That aside, what the authors
> did instead is actually pretty mind-boggling: they replaced the droplet
> with a cylinder by making the system periodic in the out-of-plane direction.
>
> This mailing list is probably not a great place for me to state my opinion
> on this (terrible) paper, but one can indeed do what the authors did. Just
> keep in mind that this is no longer a droplet, because the surface not
> facing the substrate has been removed.
>
> However, the good news is that you can indeed (partially) simulate
> atmospheric pressure this way. To do this in Gromacs, simply use
> 'pcoupltype = semiisotropic' and supply a very low compressibility value in
> the in-plane direction.
>
> Alex
>
>
>
> On 3/5/2017 12:27 AM, Rajorshi Paul wrote:
>
>> Thanks for your input. I am studying how a nano droplet spreads on a
>> substrate. I have created a four atomic layer thick FCC lattice surface on
>> which I have introduced water molecules. The entire system is placed
>> inside
>> a box of dimensions 15 nm X 15 nm X 10 nm. The system is similar to the
>> one
>> used in the following article:
>> https://www.cambridge.org/core/journals/journal-of-fluid-
>> mechanics/article/div-classtitlea-molecular-view-of-tanneran
>> daposs-law-molecular-dynamics-simulations-of-droplet-
>> spreadingdiv/E4C863EE2CFE2E17B343D0AAE85D2BB4
>> I am interested in simulating normal atmospheric conditions in my study.
>>
>> On 4 March 2017 at 23:30, Alex <nedomacho at gmail.com> wrote:
>>
>> Once again, please describe your system in more detail, because this isn't
>>> about Gromacs (which will correctly refuse pressure coupling for a
>>> finite,
>>> deep-nanoscale system). It is about the meaning of where pressure comes
>>> from in simulations and in reality.
>>>
>>> In a realistic system "1 bar" would come from the air environment + any
>>> water evaporation in equilibrium with the liquid phase of the droplet.
>>> Even
>>> if you made your surface periodic, pressure coupling would have nothing
>>> to
>>> do with your finite droplet -- it would be in vacuum. Consider this work,
>>> for instance: http://www.nature.com/nmat/jou
>>> rnal/v15/n1/abs/nmat4449.html
>>>
>>> Alex
>>>
>>>
>>>
>>> On 3/4/2017 11:17 PM, Rajorshi Paul wrote:
>>>
>>> Hi Alex,
>>>>
>>>> Like I mentioned, my system consists of a water nano drop on a
>>>> substrate.
>>>> I
>>>> need my system to be at 1 bar and 298 K. Without pressure coupling, I am
>>>> unable to set the pressure to be at 1 bar.
>>>>
>>>> On 4 March 2017 at 22:18, Alex <nedomacho at gmail.com> wrote:
>>>>
>>>> 1. Could you please provide a physical equivalent of a non-periodic NPT
>>>>
>>>>> system?
>>>>> 2. Why can't you turn off the barostat, like GMX is asking?
>>>>>
>>>>> Alex
>>>>>
>>>>>
>>>>> On 3/4/2017 8:40 PM, Rajorshi Paul wrote:
>>>>>
>>>>> I am trying to simulate water nano droplet spreading on an FCC crystal
>>>>>
>>>>>> substrate. I have not implemented periodic boundary conditions as my
>>>>>> system
>>>>>> is non-periodic. But when I tried to equilibrate my system in NPT
>>>>>> ensemble,
>>>>>> the program gives me a warning that I should set pressure coupling as
>>>>>> "no".
>>>>>> Is it possible to run NPT equilibration in non-periodic system?
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> Raj.
>>>>>>
>>>>>> --
>>>>>>
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>>>>>
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>>
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-- 
*Rajorshi Paul *
B.Tech. (Hons.), Gold Medallist (IIT Kharagpur)
First year Master of Science student
Mechanical Engineering Department
University of Alberta
Edmonton, Alberta
Canada.
Office: NINT 6-17
Email: rajorshipaul.iitkgp at gmail.com
Phone: +1 780 782 4744