[gmx-users] NPT equilibration without pbc

[Alex]

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-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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