[gmx-users] Superparamagnetism

Hi everyone, Is it possible to simulate* superparamagnetism* in Gromacs? thanks for answer. -- 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

[gmx-users] anisotropic polarization

Hi, Is anisotropic polarization implemented in Gromacs. I find a paper by Justin; ''Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model'' How can I apply it to my own molecules? Thank you for help. -- Gromacs Users

Re: [gmx-users] eelctric field

btain the pressure as if no electric field were applied, running > another simulation with the field switched off > is the only way. > > > Best, > > Christian > > On 11/15/19 3:20 PM, Amin Rouy wrote: > > Dear Christian, > > > > Thank you for the answer. My last quest

Re: [gmx-users] eelctric field

; other half downwards along the z-direction, > which will in turn affect the pressure. > > > Best, > > Christian > > On 11/13/19 3:39 PM, Amin Rouy wrote: > > Dear Christian, > > > > Thank you for your reply. However, still it is not fully clear to me. >

Re: [gmx-users] applied electirc field with use potential

options, there > is already an additional force added to all > the forces on the atoms that makes the system respond to an electric > field. You would not have to modify any other > potential to include an external electric field. > > > Best, > > Christian > > On 11/14/1

[gmx-users] applied electirc field with use potential

Hi, I have a system with a user-potential. -Can I use an external applied field? -Can I modify my user potential to include the external field? thank you for help, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] eelctric field

wever, when applying an electric field, > you would expect a different result from an > analysis with gmx potential than without electric field, because your > system will respond to the applied electric field. > > > Best, > > Christian > > On 11/13/19 2:44 PM, Amin Rou

Re: [gmx-users] eelctric field

sorry I use gromacs/2016.1. On Wed, Nov 13, 2019 at 2:44 PM Amin Rouy wrote: > Hi, > > I am using gromacs 5.0.4. I apply a uniform electric field in x direction > of my box (no walls), > E-x= 1 10 0, and simulation runs without error. > I notice that the values of electrosta

[gmx-users] eelctric field

Hi, I am using gromacs 5.0.4. I apply a uniform electric field in x direction of my box (no walls), E-x= 1 10 0, and simulation runs without error. I notice that the values of electrostatic interactions I get from the simulation is the same as without the an electric field. Which is strange,

Re: [gmx-users] shift in trajectory

Dear Justin, Yes, they form a clear phase separation. Well, I did not clearly understand your last suggestion. I do not need to have their COM coordinate, I need COM of 'A' stays in the middle of the box. On Thu, Oct 17, 2019 at 5:17 PM Justin Lemkul wrote: > > > On 10/17/19 8:04 AM,

Re: [gmx-users] shift in trajectory

it with vitalizing and moreover from gmx density outcome. On Thu, Oct 17, 2019 at 12:31 PM Justin Lemkul wrote: > > > On 10/17/19 5:24 AM, Amin Rouy wrote: > > Dear Justin, > > > > Thank you for detailed answer. However, I am still struggling and none of > > these

Re: [gmx-users] shift in trajectory

e residue of interest to be chosen for > centering. > > -Justin > > > > > Lara > > > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on

[gmx-users] shift in trajectory

Hi, I want to shift my trajectory such that the center of mass of residue 'A' locates in the center of my rectangular box. I have tries all flags in gmx trjconv, but could not succeed. Any help would be appreciated. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] tcaf

Hi everyone, Concerning viscosity calculation from TCAF method, I read in manual that: ''The fit weights decay exponentially with time constant w (given with -wt) as exp (−t/w), and the TCAF and fit are calculated up to time 5 ∗ w.'' So, 5*w is 25 ps for default value. What is the relation

Re: [gmx-users] heat capacity collection

). On Tue, Jul 16, 2019 at 9:32 PM David van der Spoel wrote: > Den 2019-07-16 kl. 13:30, skrev Amin Rouy: > > Hi everyone, > > > > I try to collect the heat capacities from my set of simulations. I see > that > > the heat capacity through gmx energy -fluct_props does

[gmx-users] heat capacity collection

Hi everyone, I try to collect the heat capacities from my set of simulations. I see that the heat capacity through gmx energy -fluct_props does not provide an output file with the heat capacities. Any suggestion how can I collect them (or how to do with an script)? thanks -- Gromacs Users

Re: [gmx-users] carbon dioxide model does not provide valid ideal-gas pressure

I should add that the problem occurs only in NPT simulation, not in NVT. It is not only about ideal-gas case, the pressure is not correct for interactive case too, as soon as it couples to barostat. On Wed, Jul 3, 2019 at 10:19 AM Amin Rouy wrote: > Hi, > > I work with carbon dioxide

[gmx-users] carbon dioxide model does not provide valid ideal-gas pressure

Hi, I work with carbon dioxide topology modeled by Justin in his tutorial page. For a very simple case, I try it with zero charge and zero interaction and expect the ideal-gas equation of state to be occurred. But it does not. To my trial and errors it seems the pressure is calculated with a bug.

[gmx-users] em.mdp

Hi, I have finished my simulations with coulombtype=PME, but just realized that in em.mdp I incorrectly had coulombtype=cut-off . Is the results incorrect now? and should I re-do my simulations? Thank you for help -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] gmx grompp

Thank you Justin. Yes, you are right as i noticed when tested the simulations with -t and without. However, i think it is not dangreous physically and the final results remain the same. Am i right? On Tue, Apr 16, 2019, 01:05 Justin Lemkul wrote: > > > On 4/15/19 8:36 AM, Amin R

[gmx-users] gmx grompp

Hi, Providing -t flag in grompp (gmx grompp -t nvt.cpt) is optional according to documentation. How does it influence on results? I'm asking because I have finished my simulation and only gave -c nvt.gro, not -t npt.cpt. Are my results correct? thanks for reply -- Gromacs Users mailing list *

[gmx-users] gmx analyze -av

Hi, I notice that the flag ''-av'' in gmx analyze does not give the average value of the set, rather the data file itself. -- 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

Re: [gmx-users] script

sorry for that. > If I understand correctly, you are working with Gromacs so you should > understand what is the .mdp file used for and there, the document of > temperature section talk about that. > > > On Thu, Mar 7, 2019 at 4:06 PM Amin Rouy wrote: > > > Thank you Justin. > >

Re: [gmx-users] script

tilizing documentation and web searching, but I > would argue this is not one of them. > > > On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy wrote: > > > >> Hi > >> > >> I would like to change the temperature of the simulation (NPT.mdp) > inside >

[gmx-users] script

Hi I would like to change the temperature of the simulation (NPT.mdp) inside my bash script, any one has idea? thanks -- 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

Re: [gmx-users] gmx tcaf directions

any help please? On Fri, Feb 8, 2019 at 12:39 PM Amin Rouy wrote: > gmx tcaf > > http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-tcaf.html > > On Fri, Feb 8, 2019 at 11:48 AM Benson Muite wrote: > >> Which part of the manual does this refer to? >> &g

Re: [gmx-users] gmx tcaf directions

gmx tcaf http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-tcaf.html On Fri, Feb 8, 2019 at 11:48 AM Benson Muite wrote: > Which part of the manual does this refer to? > > On 2/8/19 12:42 PM, Amin Rouy wrote: > > Hi, > > > > I am sorry, but the manual is

[gmx-users] gmx tcaf directions

Hi, I am sorry, but the manual is not clear to me. Does Tcaf calculates the viscosity in all x,y,z directions? the manual says: Transverse currents are calculated using the k-vectors (1,0,0) and (2,0,0) each also in the *y*- and *z*-direction -- Gromacs Users mailing list * Please search the

[gmx-users] TCAF

Hi, I have a system with an applied electric filed in x direction. I need to calculate viscosity in x direction too. How can I obtain viscosity in x direction using Tcaf? appreciate the reply, -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] rmsd,

by showing specific dynamic property, if so what that can be? On Thu, May 31, 2018 at 7:37 PM, Justin Lemkul wrote: > > > On 5/31/18 1:32 PM, Amin Rouy wrote: > >> could you please specify exactly which properties I should check? >> > > No, because this is your job

Re: [gmx-users] rmsd,

Lemkul wrote: > > > On 5/31/18 1:26 PM, Amin Rouy wrote: > >> Thanks Justin. >> I find in some literature that RMSD is not a good parameter to specify >> equilibrium from it. (e.g. >> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145956/). >> So what is t

Re: [gmx-users] rmsd,

wrote: > > > On 5/31/18 1:18 PM, Amin Rouy wrote: > >> Hi everyone, >> >> The results of simulation show all quantities are at equilibrium, like >> energies, temperature, density, etc. But RMSD is increasing all the time >> and not reaching an equilib

[gmx-users] rmsd,

Hi everyone, The results of simulation show all quantities are at equilibrium, like energies, temperature, density, etc. But RMSD is increasing all the time and not reaching an equilibrium. Does it mean should I wait longer? thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Poisson equation, Hydrodynamic interaction

Thank you very much dear Alex and David. I got my answers. On Sun, Mar 25, 2018 at 12:40 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Den 2018-03-24 kl. 23:45, skrev Amin Rouy: > >> Dear Mark, I have already checked the manual then wrote the question here. >> &

Re: [gmx-users] Poisson equation, Hydrodynamic interaction

in a fluid? On Sat, Mar 24, 2018 at 9:48 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Den 2018-03-24 kl. 20:29, skrev Amin Rouy: > >> Hi, >> >> I have 2 questions please? >> >> 1- Is Gromacs able to simulate metallic system (Poisson equation s

Re: [gmx-users] Poisson equation, Hydrodynamic interaction

Hi, I have 2 questions please? 1- Is Gromacs able to simulate metallic system (Poisson equation should be solved at the surface) 2- is Gromacs able to calculate hydrodynamic interactions? thanks. On Fri, Mar 23, 2018 at 1:04 PM, Amin Rouy <aminrou1...@gmail.com> wrote: > Hi, >

[gmx-users] Poisson equation, Hydrodynamic interaction

Hi, I have 2 questions please? 1- Does Gromacs ability to solve Poisson equation, e.g. boundary condition on metal surface? 2- is Gromacs able to calculate hydrodynamic interactions? thanks -- Gromacs Users mailing list * Please search the archive at

[gmx-users] metal surface

Hi everyone, Does Gromacs ability to simulate metal surface in presence of solvent? any method or force-field to include quantum interactions? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Comm-mode

Thank you very much. On Mar 12, 2018 14:51, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 3/12/18 9:48 AM, Amin Rouy wrote: > >> Ahan, thanks Justin. Is it default in all versions of Gromacs? >> > > As far as I remember, yes, but don't take m

Re: [gmx-users] Comm-mode

ial. Those .mdp >> files are already complicated enough for a beginner. >> > > Indeed, and comm-mode = linear is the default behavior, so it works just > fine without bothering the user to think about such abstract concepts :) > > -Justin > > > Mark >&

Re: [gmx-users] Comm-mode

> Hi, > > If you get this wrong, the equipartition of energy is usually broken and > the simulation is probably unphysical. > > Mark > > On Mon, Mar 12, 2018, 13:47 Amin Rouy <aminrou1...@gmail.com> wrote: > > > Dear Justin, > > > > If we do

Re: [gmx-users] Comm-mode

thank you so much. On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/10/18 12:31 PM, Amin Rouy wrote: > >> Thank you Justin. >> What if we do not know the phase of the final result? of if we are in 2 >> phase region (gas-liqui

Re: [gmx-users] Comm-mode

Thank you Justin. What if we do not know the phase of the final result? of if we are in 2 phase region (gas-liquid) On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/10/18 12:17 PM, Amin Rouy wrote: > >> Dear Gromacs people, >&g

[gmx-users] Comm-mode

Dear Gromacs people, I have a question please. In which condition we must use center of mass removal? Is that optional or necessary? and how to know which mode (linear or angular) is better for our simulations? Many thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] parallelization

e rank per simulation. > > Mark > > On Fri, Mar 2, 2018 at 3:00 PM Amin Rouy <aminrou1...@gmail.com> wrote: > > > sorry Justin, I am familiar with this information in the link. But I do > not > > know * I/O* and *MPI-IO* which is not in the link ?

Re: [gmx-users] Equilibration

Thanks Justin, however, > >> I run a simulation of a solute in water. I have 2 question please: >> >> 1- After NVT equilibrium, I see that all quantities like energies and >> temperature become stable, except pressure. Should I continue till >> pressure >> also goes stable? or can I move forward

Re: [gmx-users] Equilibration

any steps of equilibration you want to run. > You need to run production run when your configuration is reasonable and in > which condition, which ensemble you want to mimic > > On Wed, Feb 28, 2018 at 3:54 PM, Amin Rouy <aminrou1...@gmail.com> wrote: > > > Hi, > > > >

[gmx-users] Equilibration

Hi, I run a simulation of a solute in water. I have 2 questions please: 1- After NVT equilibrium, I see that all quantities like energies and temperature become stable, except pressure. Should I continue untill pressure becomes stable too? or can I move forward and do it in production run? 2-

[gmx-users] Equilibration

Hi, I run a simulation of a solute in water. I have 2 question please: 1- After NVT equilibrium, I see that all quantities like energies and temperature become stable, except pressure. Should I continue till pressure also goes stable? or can I move forward and do it in production run? 2- My

[gmx-users] equal systems

Hello, Which physical quantities must be equal in simulation results of two systems in order to say they are physically equal (or which quantities are enough to check)? Best, -- Gromacs Users mailing list * Please search the archive at