Re: [gmx-users] Surface tension for water

[André Farias de Moura]

I cannot understand the point of performing NPT coupling to compute surface
tension, the usual approach relies on NVT simulations instead. You might
want to take a look at this very nice investigation of the surface tension
of many water models (all done using GROMACS at constant NVT conditions):

http://rabida.uhu.es/dspace/bitstream/handle/10272/9574/Surface_tension.pdf?sequence=2

In principle, you could couple the lateral pressure to an external bath
with the exact surface tension of your model, then mechanical equilibrium
should be attained, but pressure varies wildly during MD simulations, so
actual mechanical equilibrium might not happen so easily (it seems to be
your case)

besides, your are coupling to the experimental surface tension of water,
whereas any water model has a different surface tension (usually smaller
than the experimental value). If you couple your system to a lateral
surface tension much different from what should be its equilibrium surface
tension during an MD simulation, then you are in fact applying a net
lateral pressure different from zero and again I guess this is why you are
getting your simulations crashing with high T and P values.

So unless you have a very clear idea of why you might want to perform that
simulation with a surface tension coupling, I would strongly suggest you to
use NVT instead.

IMNSHO surface tension coupling only makes sense if the liquid (whether
water or any other subphase you might be interested in) can support a
insoluble (or at least poorly soluble) film on each interface (film meaning
either monolayers, bilayers, multilayers or just another immiscible
liquid, maybe a solid state too, depending on P and T range).

I hope it helps

Andre

On Wed, Aug 30, 2017 at 2:26 AM, Iman Ahmadabadi  wrote:

> Dear Dan,
>
> As you can see in the images I sent to you, there is no error massage in
> output files. The properties of the system such as pressure or temperature
> is so high, that's why I've concluded that the system is crashed.
>
> Sincerely,
> Iman
>
> On Wed, Aug 30, 2017 at 12:44 AM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
> > Hi Dan,
> >
> > There is no error massage, It's just a crashing and stopping the
> > simulation. The version is 4.6.0.
> >
> > Iman
> >
> > On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi <
> > imanahmadabad...@gmail.com> wrote:
> >
> >> Dear Dan,
> >>
> >> I have attached the NPT.mdp file in the following:
> >>
> >> title =  NPT equilibration
> >> ; Run parameters
> >> integrator = md
> >> nsteps = 2000
> >> dt= 0.001
> >>
> >> ; Output control
> >> nstxout = 500
> >> nstvout = 500
> >> nstenergy = 500
> >> nstlog = 500
> >>
> >> ; Bond parameters
> >> continuation= no
> >> constraint_algorithm= lincs
> >> constraints= all-bonds
> >> lincs_iter= 1
> >> lincs_order= 4
> >>
> >> ; Neighborsearching
> >> cutoff-scheme   = Verlet
> >> ns_type= grid
> >> nstlist= 20
> >> rlist   = 2.0
> >> rcoulomb= 2.0
> >> rvdw= 2.0
> >>
> >> ; Electrostatics
> >> coulombtype= PME
> >> pme_order= 4
> >> fourierspacing = 0.12
> >>
> >> ; Temperature coupling is on
> >> tcoupl = V-rescale
> >> tc-grps = system
> >> tau_t = 0.1
> >> ref_t = 298.15
> >>
> >> ; Pressure coupling is on
> >> pcoupl= berendsen
> >> pcoupltype= surface-tension
> >> tau_p= 2.0  2.0
> >> ref_p= 1440  1.0
> >> compressibility = 4.46e-5  0
> >> refcoord_scaling= com
> >>
> >> ; Periodic boundary conditions
> >> pbc = xyz
> >>
> >> ; Dispersion correction
> >> DispCorr = EnerPres
> >>
> >> ; Velocity generation
> >> gen_vel = yes
> >> lincs_warnangle = 90
> >>
> >>
> >> Now I'm gonna using semiisotropic instead of surface tension like in the
> >> following:
> >> pcoupltyp   = semiisotropic
> >> tau_p = 0.5
> >> ref_p  = 1.0  1.0
> >> compressibility = 4.46e-5  0
> >>
> >> Thank you for your help.
> >> Sincerely,
> >> Iman
> >>
> >> On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi <
> >> imanahmadabad...@gmail.com> wrote:
> >>
> >>> Dear All Users,
> >>>
> >>> I'm calculating the surface tension of the water, my box contains
> almost
> >>> 5000 water molecule in the middle of that. Through NVT equilibration,
> I got
> >>> reasonable results for surface tension but when I use NPT for my
> system,
> >>> the system crashes every time. The pressure coupling options are in the
> >>> following:
> >>>
> >>> pcoupltyp = surface-tension
> >>> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
> >>> three values)
> >>> ref_p  = 1440  1.0
> >>> compressibility = 4.46e-5  0
> >>>
> >>> first ref-p value is 720*2 = 1440. 720 is the surface tension of water
> >>> in 298.15.
> >>>
> >>> Now, I'm going to use semiisotropic for P-coupling:
> >>>
> >>> pcoupltyp   = semiisotropic
> >>> tau_p = 

Re: [gmx-users] Surface tension for water

[Iman Ahmadabadi]

Dear Dan,

As you can see in the images I sent to you, there is no error massage in
output files. The properties of the system such as pressure or temperature
is so high, that's why I've concluded that the system is crashed.

Sincerely,
Iman

On Wed, Aug 30, 2017 at 12:44 AM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:

> Hi Dan,
>
> There is no error massage, It's just a crashing and stopping the
> simulation. The version is 4.6.0.
>
> Iman
>
> On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Dan,
>>
>> I have attached the NPT.mdp file in the following:
>>
>> title =  NPT equilibration
>> ; Run parameters
>> integrator = md
>> nsteps = 2000
>> dt= 0.001
>>
>> ; Output control
>> nstxout = 500
>> nstvout = 500
>> nstenergy = 500
>> nstlog = 500
>>
>> ; Bond parameters
>> continuation= no
>> constraint_algorithm= lincs
>> constraints= all-bonds
>> lincs_iter= 1
>> lincs_order= 4
>>
>> ; Neighborsearching
>> cutoff-scheme   = Verlet
>> ns_type= grid
>> nstlist= 20
>> rlist   = 2.0
>> rcoulomb= 2.0
>> rvdw= 2.0
>>
>> ; Electrostatics
>> coulombtype= PME
>> pme_order= 4
>> fourierspacing = 0.12
>>
>> ; Temperature coupling is on
>> tcoupl = V-rescale
>> tc-grps = system
>> tau_t = 0.1
>> ref_t = 298.15
>>
>> ; Pressure coupling is on
>> pcoupl= berendsen
>> pcoupltype= surface-tension
>> tau_p= 2.0  2.0
>> ref_p= 1440  1.0
>> compressibility = 4.46e-5  0
>> refcoord_scaling= com
>>
>> ; Periodic boundary conditions
>> pbc = xyz
>>
>> ; Dispersion correction
>> DispCorr = EnerPres
>>
>> ; Velocity generation
>> gen_vel = yes
>> lincs_warnangle = 90
>>
>>
>> Now I'm gonna using semiisotropic instead of surface tension like in the
>> following:
>> pcoupltyp   = semiisotropic
>> tau_p = 0.5
>> ref_p  = 1.0  1.0
>> compressibility = 4.46e-5  0
>>
>> Thank you for your help.
>> Sincerely,
>> Iman
>>
>> On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi <
>> imanahmadabad...@gmail.com> wrote:
>>
>>> Dear All Users,
>>>
>>> I'm calculating the surface tension of the water, my box contains almost
>>> 5000 water molecule in the middle of that. Through NVT equilibration, I got
>>> reasonable results for surface tension but when I use NPT for my system,
>>> the system crashes every time. The pressure coupling options are in the
>>> following:
>>>
>>> pcoupltyp = surface-tension
>>> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
>>> three values)
>>> ref_p  = 1440  1.0
>>> compressibility = 4.46e-5  0
>>>
>>> first ref-p value is 720*2 = 1440. 720 is the surface tension of water
>>> in 298.15.
>>>
>>> Now, I'm going to use semiisotropic for P-coupling:
>>>
>>> pcoupltyp   = semiisotropic
>>> tau_p = 0.5
>>> ref_p  = 1.0  1.0
>>> compressibility = 4.46e-5  0
>>>
>>> Could I have any recommendation about my problem with surface-tension
>>> pcoupltyp? Am I right with semiisotropic options?
>>>
>>>
>>> Respectfully,
>>> Iman Ahmadabadi
>>>
>>
>>
>>
>> --
>> Iman Ahmadabadi
>>
>> Sharif University of Technology, Tehran, Iran
>>
>> Department of Physics and Chemistry
>>
>> Phone: (+98) 9156125273
>>
>> Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
>>
>
>
>
> --
> Iman Ahmadabadi
>
> Sharif University of Technology, Tehran, Iran
>
> Department of Physics and Chemistry
>
> Phone: (+98) 9156125273
>
> Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
>



-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Phone: (+98) 9156125273

Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
-- 
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Re: [gmx-users] Surface tension for water

[Dan Gil]

Iman,

You get the error message in the terminal if you are running it on your own
machine. If you are running on a supercomputer, the error messages will be
directed to a file. How do you know the simulation is crashing without the
software telling you? Please find the message (check all outputs), wherever
it might be, and share it with us. Otherwise I don't know what the problem
could be.

Dan

On Tue, Aug 29, 2017 at 4:14 PM, Iman Ahmadabadi  wrote:

> Hi Dan,
>
> There is no error massage, It's just a crashing and stopping the
> simulation. The version is 4.6.0.
>
> Iman
>
> On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com
> > wrote:
>
> > Dear Dan,
> >
> > I have attached the NPT.mdp file in the following:
> >
> > title =  NPT equilibration
> > ; Run parameters
> > integrator = md
> > nsteps = 2000
> > dt= 0.001
> >
> > ; Output control
> > nstxout = 500
> > nstvout = 500
> > nstenergy = 500
> > nstlog = 500
> >
> > ; Bond parameters
> > continuation= no
> > constraint_algorithm= lincs
> > constraints= all-bonds
> > lincs_iter= 1
> > lincs_order= 4
> >
> > ; Neighborsearching
> > cutoff-scheme   = Verlet
> > ns_type= grid
> > nstlist= 20
> > rlist   = 2.0
> > rcoulomb= 2.0
> > rvdw= 2.0
> >
> > ; Electrostatics
> > coulombtype= PME
> > pme_order= 4
> > fourierspacing = 0.12
> >
> > ; Temperature coupling is on
> > tcoupl = V-rescale
> > tc-grps = system
> > tau_t = 0.1
> > ref_t = 298.15
> >
> > ; Pressure coupling is on
> > pcoupl= berendsen
> > pcoupltype= surface-tension
> > tau_p= 2.0  2.0
> > ref_p= 1440  1.0
> > compressibility = 4.46e-5  0
> > refcoord_scaling= com
> >
> > ; Periodic boundary conditions
> > pbc = xyz
> >
> > ; Dispersion correction
> > DispCorr = EnerPres
> >
> > ; Velocity generation
> > gen_vel = yes
> > lincs_warnangle = 90
> >
> >
> > Now I'm gonna using semiisotropic instead of surface tension like in the
> > following:
> > pcoupltyp   = semiisotropic
> > tau_p = 0.5
> > ref_p  = 1.0  1.0
> > compressibility = 4.46e-5  0
> >
> > Thank you for your help.
> > Sincerely,
> > Iman
> >
> > On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi <
> > imanahmadabad...@gmail.com> wrote:
> >
> >> Dear All Users,
> >>
> >> I'm calculating the surface tension of the water, my box contains almost
> >> 5000 water molecule in the middle of that. Through NVT equilibration, I
> got
> >> reasonable results for surface tension but when I use NPT for my system,
> >> the system crashes every time. The pressure coupling options are in the
> >> following:
> >>
> >> pcoupltyp = surface-tension
> >> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
> >> three values)
> >> ref_p  = 1440  1.0
> >> compressibility = 4.46e-5  0
> >>
> >> first ref-p value is 720*2 = 1440. 720 is the surface tension of water
> in
> >> 298.15.
> >>
> >> Now, I'm going to use semiisotropic for P-coupling:
> >>
> >> pcoupltyp   = semiisotropic
> >> tau_p = 0.5
> >> ref_p  = 1.0  1.0
> >> compressibility = 4.46e-5  0
> >>
> >> Could I have any recommendation about my problem with surface-tension
> >> pcoupltyp? Am I right with semiisotropic options?
> >>
> >>
> >> Respectfully,
> >> Iman Ahmadabadi
> >>
> >
> >
> >
> > --
> > Iman Ahmadabadi
> >
> > Sharif University of Technology, Tehran, Iran
> >
> > Department of Physics and Chemistry
> >
> > Phone: (+98) 9156125273
> >
> > Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
> >
>
>
>
> --
> Iman Ahmadabadi
>
> Sharif University of Technology, Tehran, Iran
>
> Department of Physics and Chemistry
>
> Phone: (+98) 9156125273
>
> Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
> --
> 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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Re: [gmx-users] Surface tension for water

[Iman Ahmadabadi]

Hi Dan,

There is no error massage, It's just a crashing and stopping the
simulation. The version is 4.6.0.

Iman

On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi  wrote:

> Dear Dan,
>
> I have attached the NPT.mdp file in the following:
>
> title =  NPT equilibration
> ; Run parameters
> integrator = md
> nsteps = 2000
> dt= 0.001
>
> ; Output control
> nstxout = 500
> nstvout = 500
> nstenergy = 500
> nstlog = 500
>
> ; Bond parameters
> continuation= no
> constraint_algorithm= lincs
> constraints= all-bonds
> lincs_iter= 1
> lincs_order= 4
>
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type= grid
> nstlist= 20
> rlist   = 2.0
> rcoulomb= 2.0
> rvdw= 2.0
>
> ; Electrostatics
> coulombtype= PME
> pme_order= 4
> fourierspacing = 0.12
>
> ; Temperature coupling is on
> tcoupl = V-rescale
> tc-grps = system
> tau_t = 0.1
> ref_t = 298.15
>
> ; Pressure coupling is on
> pcoupl= berendsen
> pcoupltype= surface-tension
> tau_p= 2.0  2.0
> ref_p= 1440  1.0
> compressibility = 4.46e-5  0
> refcoord_scaling= com
>
> ; Periodic boundary conditions
> pbc = xyz
>
> ; Dispersion correction
> DispCorr = EnerPres
>
> ; Velocity generation
> gen_vel = yes
> lincs_warnangle = 90
>
>
> Now I'm gonna using semiisotropic instead of surface tension like in the
> following:
> pcoupltyp   = semiisotropic
> tau_p = 0.5
> ref_p  = 1.0  1.0
> compressibility = 4.46e-5  0
>
> Thank you for your help.
> Sincerely,
> Iman
>
> On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear All Users,
>>
>> I'm calculating the surface tension of the water, my box contains almost
>> 5000 water molecule in the middle of that. Through NVT equilibration, I got
>> reasonable results for surface tension but when I use NPT for my system,
>> the system crashes every time. The pressure coupling options are in the
>> following:
>>
>> pcoupltyp = surface-tension
>> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
>> three values)
>> ref_p  = 1440  1.0
>> compressibility = 4.46e-5  0
>>
>> first ref-p value is 720*2 = 1440. 720 is the surface tension of water in
>> 298.15.
>>
>> Now, I'm going to use semiisotropic for P-coupling:
>>
>> pcoupltyp   = semiisotropic
>> tau_p = 0.5
>> ref_p  = 1.0  1.0
>> compressibility = 4.46e-5  0
>>
>> Could I have any recommendation about my problem with surface-tension
>> pcoupltyp? Am I right with semiisotropic options?
>>
>>
>> Respectfully,
>> Iman Ahmadabadi
>>
>
>
>
> --
> Iman Ahmadabadi
>
> Sharif University of Technology, Tehran, Iran
>
> Department of Physics and Chemistry
>
> Phone: (+98) 9156125273
>
> Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
>



-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Phone: (+98) 9156125273

Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
-- 
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Surface tension for water

[Iman Ahmadabadi]

Dear Dan,

I have attached the NPT.mdp file in the following:

title =  NPT equilibration
; Run parameters
integrator = md
nsteps = 2000
dt= 0.001

; Output control
nstxout = 500
nstvout = 500
nstenergy = 500
nstlog = 500

; Bond parameters
continuation= no
constraint_algorithm= lincs
constraints= all-bonds
lincs_iter= 1
lincs_order= 4

; Neighborsearching
cutoff-scheme   = Verlet
ns_type= grid
nstlist= 20
rlist   = 2.0
rcoulomb= 2.0
rvdw= 2.0

; Electrostatics
coulombtype= PME
pme_order= 4
fourierspacing = 0.12

; Temperature coupling is on
tcoupl = V-rescale
tc-grps = system
tau_t = 0.1
ref_t = 298.15

; Pressure coupling is on
pcoupl= berendsen
pcoupltype= surface-tension
tau_p= 2.0  2.0
ref_p= 1440  1.0
compressibility = 4.46e-5  0
refcoord_scaling= com

; Periodic boundary conditions
pbc = xyz

; Dispersion correction
DispCorr = EnerPres

; Velocity generation
gen_vel = yes
lincs_warnangle = 90


Now I'm gonna using semiisotropic instead of surface tension like in the
following:
pcoupltyp   = semiisotropic
tau_p = 0.5
ref_p  = 1.0  1.0
compressibility = 4.46e-5  0

Thank you for your help.
Sincerely,
Iman

On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi  wrote:

> Dear All Users,
>
> I'm calculating the surface tension of the water, my box contains almost
> 5000 water molecule in the middle of that. Through NVT equilibration, I got
> reasonable results for surface tension but when I use NPT for my system,
> the system crashes every time. The pressure coupling options are in the
> following:
>
> pcoupltyp = surface-tension
> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
> three values)
> ref_p  = 1440  1.0
> compressibility = 4.46e-5  0
>
> first ref-p value is 720*2 = 1440. 720 is the surface tension of water in
> 298.15.
>
> Now, I'm going to use semiisotropic for P-coupling:
>
> pcoupltyp   = semiisotropic
> tau_p = 0.5
> ref_p  = 1.0  1.0
> compressibility = 4.46e-5  0
>
> Could I have any recommendation about my problem with surface-tension
> pcoupltyp? Am I right with semiisotropic options?
>
>
> Respectfully,
> Iman Ahmadabadi
>



-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Phone: (+98) 9156125273

Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
-- 
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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Re: [gmx-users] Surface tension for water

[Dan Gil]

What is the error message?
What version of Gromacs are you using?
Can you post the entire .mdp file?


On Tue, Aug 29, 2017 at 9:34 AM, Iman Ahmadabadi  wrote:

> Dear All Users,
>
> I'm calculating the surface tension of the water, my box contains almost
> 5000 water molecule in the middle of that. Through NVT equilibration, I got
> reasonable results for surface tension but when I use NPT for my system,
> the system crashes every time. The pressure coupling options are in the
> following:
>
> pcoupltyp = surface-tension
> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all three
> values)
> ref_p  = 1440  1.0
> compressibility = 4.46e-5  0
>
> first ref-p value is 720*2 = 1440. 720 is the surface tension of water in
> 298.15.
>
> Now, I'm going to use semiisotropic for P-coupling:
>
> pcoupltyp   = semiisotropic
> tau_p = 0.5
> ref_p  = 1.0  1.0
> compressibility = 4.46e-5  0
>
> Could I have any recommendation about my problem with surface-tension
> pcoupltyp? Am I right with semiisotropic options?
>
>
> Respectfully,
> Iman Ahmadabadi
> --
> 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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[gmx-users] Surface tension for water

[Iman Ahmadabadi]

Dear All Users,

I'm calculating the surface tension of the water, my box contains almost
5000 water molecule in the middle of that. Through NVT equilibration, I got
reasonable results for surface tension but when I use NPT for my system,
the system crashes every time. The pressure coupling options are in the
following:

pcoupltyp = surface-tension
tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all three
values)
ref_p  = 1440  1.0
compressibility = 4.46e-5  0

first ref-p value is 720*2 = 1440. 720 is the surface tension of water in
298.15.

Now, I'm going to use semiisotropic for P-coupling:

pcoupltyp   = semiisotropic
tau_p = 0.5
ref_p  = 1.0  1.0
compressibility = 4.46e-5  0

Could I have any recommendation about my problem with surface-tension
pcoupltyp? Am I right with semiisotropic options?


Respectfully,
Iman Ahmadabadi
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