[gmx-users] NPT equilibration without pbc

[Rajorshi Paul]

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-tannerandaposs-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/journal/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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-- 
*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