Re: [gmx-users] NPT equilibration without pbc

[Mark Abraham]

Hi,

People might find the approach at https://doi.org/10.1017/jfm.2015.517 more
rigorous!

Mark

On Mon, Mar 6, 2017 at 1:58 AM Rajorshi Paul 
wrote:

> Thanks Alex for the suggestion!!
>
> On 5 March 2017 at 01:49, Alex  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  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  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.
> >>
> >> --
> >>
> > 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
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> >
>  --
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> >>>
> >>>
> >>
> >>
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> >
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Re: [gmx-users] NPT equilibration without pbc

[Rajorshi Paul]

Thanks Alex for the suggestion!!

On 5 March 2017 at 01:49, Alex  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  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  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.
>>
>> --
>>
> 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-requ...@gromacs.org.
>
>
>
 --
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>>>
>>> * 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
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>>>
>>
>>
> --
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> * Please search the archive at http://www.gromacs.org/Support
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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.iit...@gmail.com
Phone: +1 780 782 4744
-- 
Gromacs 

Re: [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  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  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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Re: [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  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  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.

 --
>>> 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-requ...@gromacs.org.
>>>
>>>
>>
>>
> --
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>
> * 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
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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.iit...@gmail.com
Phone: +1 780 782 4744
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] NPT equilibration without pbc

[Alex]

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  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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Re: [gmx-users] NPT equilibration without pbc

[Rajorshi Paul]

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  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.
>>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
*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.iit...@gmail.com
Phone: +1 780 782 4744
-- 
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* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] NPT equilibration without pbc

[Alex]

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.


--
Gromacs Users mailing list

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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