[gmx-users] Position Dependent Electric Filed

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

[gmx-users] converting .xtc into .xyz

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

[gmx-users] Determining the cut offs more than half of the box

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

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

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

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

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

[gmx-users] SPC/Fw model of water

Dear Gromacs Users, I need the SPC/Fw model of water. Could I receive this model? Best Regards -- 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_Lis

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

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

[gmx-users] dielectric constant along specific direction

Dear Gromacs users, Does the gromacs have the ability to compute the dielectric constant along a specific direction (for example x axis)? Sincerely -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Flexible and posres

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 -- Gromacs Users mailing list * Please search the archive a

Re: [gmx-users] Flexible and posres

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,

Re: [gmx-users] Flexible and posres

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

Re: [gmx-users] Flexible and posres

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

[gmx-users] Domain Decomposition

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

[gmx-users] Inconsistent Shifts

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

Re: [gmx-users] Inconsistent Shifts

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

[gmx-users] Inconsistent Shifts

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

[gmx-users] Dielectric Constant

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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/

[gmx-users] Dielectric Constant: Theory and Implementation

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

[gmx-users] v-rescale

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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_

[gmx-users] Rotation in gmx traj

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

[gmx-users] (no subject)

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

[gmx-users] Surface tension for water

p? 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)subscri

Re: [gmx-users] Surface tension for water

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

Re: [gmx-users] Surface tension for water

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

Re: [gmx-users] Surface tension for water

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

[gmx-users] Constant Pressure just in z axis

which value should I use for each X and X/Y directions for pressure coupling? 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.o

Re: [gmx-users] Constant Pressure just in z axis

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

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

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

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

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