Re: [gmx-users] Dipole moment and dielectric constant - gmx dipoles

[Iman Ahmadabadi]

Dear Philip,

Yes, you are right, thank you very much for your time and kindness.

Best regards,
Iman

On Sun, Jan 26, 2020 at 4:17 PM Iman Ahmadabadi 
wrote:

> Dear Gromacs users,
>
> I'm trying to reproduce the gmx dipoles results via python code. In
> calculating the fluctuations of total dipole moment, which is the sum on
> dipole moment of individual molecules in the box, M = \sum q_{i}*R_{i}, in
> which the charges q_{i} are in electron unit and position R_{i} are in nm.
> For calculating M for each time step (frame), the x,y, and z component of
> each atom is multiplied to their charges, and then summing on all atoms.
> The average of M is on all trajectory frames, meaning that summing on M for
> all frames and then dividing by the number of frames. Here, the acquired M
> is divided by proper constant (0.020819434 e
> <https://en.wikipedia.org/wiki/Elementary_charge>·nm
> <https://en.wikipedia.org/wiki/Nanometre>) to set it in the Debye unit.
>
> For M^{2}, M.M (dot product of M by M) is calculated for each frame and
> then summing on all frames, followed by dividing by the number of frames.
> But the results are larger than gmx dipoles, I wanted to ask that there is
> something gmx dipoles is using in order to calculate the  and ,
> causing this difference? I appreciate any help in this regard.
>
> Best regards,
> Iman
>
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[gmx-users] Dipole moment and dielectric constant - gmx dipoles

[Iman Ahmadabadi]

Dear Gromacs users,

I'm trying to reproduce the gmx dipoles results via python code. In
calculating the fluctuations of total dipole moment, which is the sum on
dipole moment of individual molecules in the box, M = \sum q_{i}*R_{i}, in
which the charges q_{i} are in electron unit and position R_{i} are in nm.
For calculating M for each time step (frame), the x,y, and z component of
each atom is multiplied to their charges, and then summing on all atoms.
The average of M is on all trajectory frames, meaning that summing on M for
all frames and then dividing by the number of frames. Here, the acquired M
is divided by proper constant (0.020819434 e
·nm
) to set it in the Debye unit.

For M^{2}, M.M (dot product of M by M) is calculated for each frame and
then summing on all frames, followed by dividing by the number of frames.
But the results are larger than gmx dipoles, I wanted to ask that there is
something gmx dipoles is using in order to calculate the  and ,
causing this difference? I appreciate any help in this regard.

Best regards,
Iman
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[gmx-users] Rotation in gmx traj

[Iman Ahmadabadi]

Dear Users,

Which way the -ekr option in gmx traj computes the rotational kinetic
energy of solvent molecules?

1_ About their COM by the square velocity perpendicular to the position
vector of the molecules (from the point of center of mass of whole solvent
to the position of molecule) and summing on all solvent molecules?

2_ or it is the rotational kinetic energy of each molecule on its own
center individually and then summing on all molecules?

Many Thanks,
Iman
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[gmx-users] v-rescale

[Iman Ahmadabadi]

Dear Gromacs Users,

The V-rescale option for thermostat produces velocities based on Maxwell
distribution function like nose-hoover thermostat for the system?

Respectfully,
Iman
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[gmx-users] Dielectric Constant: Theory and Implementation

[Iman Ahmadabadi]

Dear Gromacs Users,

In determining the dielectric constant of water, in some similar systems that
their difference for example is in the length of the box in z direction, I
get different and also physically wrong results e.g non consistent values
between  ,  , and   and also in average volume over run, and
because of this, I'm going to read about the details of the procedure and
theory that gromacs calculates the dipole moments of molecules to
determining the dielectric constant and related parameters (e.g average
volume over run,  and  in each direction) but I cannot find the
reference or paper that these things have been explained there. May you
help me in this regard?

Respectfully,
Iman
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[gmx-users] Dielectric Constant

[Iman Ahmadabadi]

Dear Users,

I cannot find a reference about the calculation of dielectric constant. How
can I find the reference paper explains how dielectric constant is
calculated from it?

Respectfully
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[gmx-users] Inconsistent Shifts

[Iman Ahmadabadi]

Dear Dallas,

I have tried the 2016.5 version of gromacs that it has the same warning
about the inconsistent shifts. I don't know why it should arises as a
warning and what is the problem. Is there another way to fix this warning?

Sincerely
Iman

On Wed, Feb 21, 2018 at 11:26 AM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:

> Dear Dallas,
>
> Yes, the system has periodic molecules (periodic-molecules = yes) and the
> version of gromacs is 5.1.2. So, I should use for calculating the
> properties of the system by gromacs 2016 and newer ones?
>
> Respectfully,
> Iman
>
> On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Gromacs users,
>>
>> In using some commands in gromacs, the sentence "There were 240
>> inconsistent shifts. Check your topology" come up on the screen and I don't
>> know what is wrong in my topology file, however it calculates correctly the
>> features of the system but I would like to know the reason of this warning.
>>
>> Respectfully,
>> Iman
>>
>
>
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Re: [gmx-users] Inconsistent Shifts

[Iman Ahmadabadi]

Dear Dallas,

Yes, the system has periodic molecules (periodic-molecules = yes) and the
version of gromacs is 5.1.2. So, I should use for calculating the
properties of the system by gromacs 2016 and newer ones?

Respectfully,
Iman

On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi <imanahmadabad...@gmail.com
> wrote:

> Dear Gromacs users,
>
> In using some commands in gromacs, the sentence "There were 240
> inconsistent shifts. Check your topology" come up on the screen and I don't
> know what is wrong in my topology file, however it calculates correctly the
> features of the system but I would like to know the reason of this warning.
>
> Respectfully,
> Iman
>
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[gmx-users] Domain Decomposition

[Iman Ahmadabadi]

Dear Gromacs Users,

In one job, I always get in (any number of nodes) the domain decomposition
error as following and I don't know what should I do. I have to use the
-dds or -rdd setting for my problem?

Sincerely
Iman

Initializing Domain Decomposition on 56 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 9.579 nm, LJ-14, atoms 1663 1728
  multi-body bonded interactions: 9.579 nm, Angle, atoms 1727 1728
Minimum cell size due to bonded interactions: 10.537 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.700 nm
Estimated maximum distance required for P-LINCS: 0.700 nm
Guess for relative PME load: 0.87
Using 0 separate PME nodes, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 56 cells with a minimum initial size of 13.171 nm
The maximum allowed number of cells is: X 0 Y 0 Z 0

---
Program mdrun, VERSION 4.6
Source code file: /share/apps/gromacs/gromacs-4.6/src/mdlib/domdec.c, line:
6767

Fatal error:
There is no domain decomposition for 56 nodes that is compatible with the
given box and a minimum cell size of 13.1712 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
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Re: [gmx-users] Flexible and posres

[Iman Ahmadabadi]

Dear Justin and Mark,

The define = -DPOSRES -DFLEXIBLE is correct and thank you so much for your
help.

Respectfully,
Iman

On Wed, Feb 14, 2018 at 11:17 PM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:

> Dear Justin,
>
> Because there is a movement on atoms that posres should act on them, and
> this condition doesn't occur when the flexible option is not used.
>
> Sincerely,
> Iman
>
> On Wed, Feb 14, 2018 at 8:48 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Mark,
>>
>> I forgot the D in -DPOSRES in the previous email. However I used the
>> "define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint
>> was not applied on the atoms. Is there another way to solve the problem?
>>
>> Respectfully,
>> Iman
>>
>> On Wed, Feb 14, 2018 at 5:48 PM, Iman Ahmadabadi <
>> imanahmadabad...@gmail.com> wrote:
>>
>>> Dear Gromacs Users,
>>>
>>> If I wanna use some flexible bonds and also use position restraint on
>>> some other atoms, how should I do this? the error arises because 2 define =
>>> -DFLEXIBLE and -POSRES is not allowed in the .mdp files.
>>>
>>> Respectfully
>>>
>>>
>>
>
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Re: [gmx-users] Flexible and posres

[Iman Ahmadabadi]

Dear Justin,

Because there is a movement on atoms that posres should act on them, and
this condition doesn't occur when the flexible option is not used.

Sincerely,
Iman

On Wed, Feb 14, 2018 at 8:48 PM, Iman Ahmadabadi <imanahmadabad...@gmail.com
> wrote:

> Dear Mark,
>
> I forgot the D in -DPOSRES in the previous email. However I used the
> "define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint
> was not applied on the atoms. Is there another way to solve the problem?
>
> Respectfully,
> Iman
>
> On Wed, Feb 14, 2018 at 5:48 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Gromacs Users,
>>
>> If I wanna use some flexible bonds and also use position restraint on
>> some other atoms, how should I do this? the error arises because 2 define =
>> -DFLEXIBLE and -POSRES is not allowed in the .mdp files.
>>
>> Respectfully
>>
>>
>
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Re: [gmx-users] Flexible and posres

[Iman Ahmadabadi]

Dear Mark,

I forgot the D in -DPOSRES in the previous email. However I used the
"define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint
was not applied on the atoms. Is there another way to solve the problem?

Respectfully,
Iman

On Wed, Feb 14, 2018 at 5:48 PM, Iman Ahmadabadi <imanahmadabad...@gmail.com
> wrote:

> Dear Gromacs Users,
>
> If I wanna use some flexible bonds and also use position restraint on some
> other atoms, how should I do this? the error arises because 2 define =
> -DFLEXIBLE and -POSRES is not allowed in the .mdp files.
>
> Respectfully
>
>
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[gmx-users] Flexible and posres

[Iman Ahmadabadi]

Dear Gromacs Users,

If I wanna use some flexible bonds and also use position restraint on some
other atoms, how should I do this? the error arises because 2 define =
-DFLEXIBLE and -POSRES is not allowed in the .mdp files.

Respectfully
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[gmx-users] dielectric constant along specific direction

[Iman Ahmadabadi]

Dear Gromacs users,

Does the gromacs have the ability to compute the dielectric constant along
a specific direction (for example x axis)?

Sincerely
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[gmx-users] Position restraint on flexible models of water

[Iman Ahmadabadi]

Dear Gromacs users,

As you know, there is a position restraint for water molecules (on each
oxygen atom) in the topology file. what is purpose of this restraint in the
topology files?

My second question is: this position restraint should exist while I'm using
a flexible model of water or not?

Sincerely,
Iman
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[gmx-users] SPC/Fw model of water

[Iman Ahmadabadi]

Dear Gromacs Users,

I need the SPC/Fw model of water. Could I receive this model?

Best Regards
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Re: [gmx-users] Determining the cut offs more than half of the box

[Iman Ahmadabadi]

Dear Mr.Mark Abraham,

Thank you for your help.
Because of the accuracy of the results, I should use a reasonable cut offs
for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too
small for my project because of the importance of long range interactions.
The box size is an obstacle to determining the desired cut off for
interactions.

Best regards

On Sun, Nov 19, 2017 at 11:47 AM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:

> Dear Mr.Mark Abraham,
>
> Thank you for your help.
> Because of the accuracy of the results, I should use a reasonable cut offs
> for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too
> small for my project because of the importance of long range interactions.
> The box size is an obstacle to determining the desired cut off for
> interactions.
>
> Best regards
>
> On Sat, Nov 18, 2017 at 8:37 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Gromacs Users,
>>
>> I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box
>> that its height along z direction is too small (for example 2.0 nm)  but
>> the error will arise for me and I couldn't use the cut off more than 1.0 nm
>> because of the box size. What should I do in this regard?
>>
>> Best,
>>
>>
>>
>
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Re: [gmx-users] Determining the cut offs more than half of the box

[Iman Ahmadabadi]

Dear Mr.Mark Abraham,

Thank you for your help.
Because of the accuracy of the results, I should use a reasonable cut offs
for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too
small for my project because of the importance of long range interactions.
The box size is an obstacle to determining the desired cut off for
interactions.

Best regards

On Sat, Nov 18, 2017 at 8:37 PM, Iman Ahmadabadi <imanahmadabad...@gmail.com
> wrote:

> Dear Gromacs Users,
>
> I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box
> that its height along z direction is too small (for example 2.0 nm)  but
> the error will arise for me and I couldn't use the cut off more than 1.0 nm
> because of the box size. What should I do in this regard?
>
> Best,
>
>
>


-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Email: imanahmadabad...@gmail.com ,imanahmadab...@physics.sharif.edu
<ahmadabad...@ch.sharif.edu>
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[gmx-users] Determining the cut offs more than half of the box

[Iman Ahmadabadi]

Dear Gromacs Users,

I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box
that its height along z direction is too small (for example 2.0 nm)  but
the error will arise for me and I couldn't use the cut off more than 1.0 nm
because of the box size. What should I do in this regard?

Best,
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[gmx-users] converting .xtc into .xyz

[Iman Ahmadabadi]

Dear Users,

How could I convert .xtc (or .trr) file of output of a run frames into .xyz
format? my mean is to obtaining one .xyz file for whole frames that created
by run?

Respectfully

-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
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[gmx-users] Position Dependent Electric Filed

[Iman Ahmadabadi]

Dear Users,

I need to apply an electric field on a box but the field should be position
dependent, for example I should apply field E1 to the half of the box as
well as E2 to the another half while E1 and E2 are different. Could anyone
help me in this regard?

Respectfully
Iman Ahmadabadi

-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
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Re: [gmx-users] Constant Pressure just in z axis

[Iman Ahmadabadi]

Dear Christopher,

Thank you for your help, How about the value of pressure along X/Y
directions? does it matter the value of ref-p for X/Y while I use 0 for
water compressibility in X/Y direction ?

Respectfully,
Iman

On Wed, Oct 4, 2017 at 6:47 PM, Iman Ahmadabadi <imanahmadabad...@gmail.com>
wrote:

> Dear users,
>
> I would like to keep the pressure (1 bar) in the z direction and there is
> not any similar condition in X/Y directions, I mean it's not obligatory for
> keeping the pressure in a specific value in X/Y direction. Is the
> semiisotropic coupling sufficient to my purpose? If it is, which value
> should I use for each X and X/Y directions for pressure coupling?
>
> 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
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[gmx-users] Constant Pressure just in z axis

[Iman Ahmadabadi]

Dear users,

I would like to keep the pressure (1 bar) in the z direction and there is
not any similar condition in X/Y directions, I mean it's not obligatory for
keeping the pressure in a specific value in X/Y direction. Is the
semiisotropic coupling sufficient to my purpose? If it is, which value
should I use for each X and X/Y directions for pressure coupling?

Respectfully,
Iman Ahmadabadi
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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
-- 
Gromacs Users mailing list

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

[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
-- 
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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[gmx-users] (no subject)

[Iman Ahmadabadi]

Dear Users,

I'm determining my .mdp file for NPT equilibration, but I don't know how to
determine the ref_p section of mdp.

pcoupl = berendsen
pcoupltype = surface-tension
tau_p = 0.5 0.5
ref_p = 1.0 1.0
compressibility = 4.46e-5 4.46e-5

I'm gonna to calculate surface tension for a layer of water.

Sincerely,
Iman
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