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 fluc
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
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 summin
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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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
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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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 Ahmad
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 wrote:
> D
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
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
Wi
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 posre
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 wrote:
> Dear Mark,
>
> I forgot the D in -DPOSRES in the
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,
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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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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* Can't
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?
Si
Dear Gromacs Users,
I need the SPC/Fw model of water. Could I receive this model?
Best Regards
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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
obstacle to determining the desired cut off for
interactions.
Best regards
On Sat, Nov 18, 2017 at 8:37 PM, Iman Ahmadabadi 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 ex
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
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
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
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
wrote:
> Dear users,
&g
which value
should I use for each X and X/Y directions for pressure coupling?
Respectfully,
Iman Ahmadabadi
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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
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 equilibratio
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
p? Am I right with semiisotropic options?
Respectfully,
Iman Ahmadabadi
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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 wate
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