Re: [gmx-users] Electric field

Please ignore my message. I figured it out. It should be 2*pi*1 = 6.28 for omega to generate a full cycle. > On 12 Apr 2020, at 14:15, Prithwish Nandi wrote: > > Hi, > I am trying to generate an alternating e-field using gromcas input as > following: > > electric-field-x = 1.5 1 0

Re: [gmx-users] Electric field or CompEl protocol?

I think CompEl is described in the manual, the options for it are here: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html I've never used it, so I can't suggest anything, but you can ask on this board for specific mdp examples. The way CompEl works is conceptually simple:

Re: [gmx-users] Electric field or CompEl protocol?

Dear Alex! Yes, I thought about all Your reflections and I'm also not sure that CompEl is well parameterzied for a non-specialist like me and the electric field is more intuitive for me. However, when I saw the dimension 'V/nm' for the first time, I thought that something must depend on the

Re: [gmx-users] Electric field or CompEl protocol?

It's more of a philosophical question in, unfortunately. I don't use CompEl, because I believe it is conceptually clunky, but that's a matter of opinion that could turn into discussion beyond the scope of your question. I don't study biomolecules, so I can get away with applying direct fields.

Re: [gmx-users] Electric Field

Thank you I'm trying to update it for external magnetic filed applications On Sun, Feb 18, 2018 at 12:57 PM, Mark Abraham wrote: > Hi, > > Suggestion, get the git version of gromacs and use > > git grep -i -G"electric field" > > src/gromacs/applied-forces > > Mark > >

Re: [gmx-users] Electric Field

Hi, Suggestion, get the git version of gromacs and use git grep -i -G"electric field" src/gromacs/applied-forces Mark On Sun, Feb 18, 2018 at 7:36 PM Ali Ahmed wrote: > Dear Mark, > I could not find the electric field calculation code. In 2016 version, the > code was

Re: [gmx-users] Electric Field

Dear Mark, I could not find the electric field calculation code. In 2016 version, the code was in mdlib/sim_util.cpp but in 2018 version I could not find it. Is it elsewhere? can you tell me, please? Thanks On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed wrote: > Dear Mark, >

Re: [gmx-users] Electric Field

Dear Mark, Thank you. this is good I will study it. On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham wrote: > Hi, > > See section 6.7 of the 2018 reference manual for what is supported. > > MArk > > On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed wrote:

Re: [gmx-users] Electric Field

Hi, See section 6.7 of the 2018 reference manual for what is supported. MArk On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed wrote: > Hello GROMACS users > I have looked through GROMACS user manual to understand the theory behind > applying external electric field but I did not

Re: [gmx-users] Electric field unit

Seems rational! Thank you very much David. On Thu, Jan 14, 2016 at 7:20 PM, mah maz wrote: > Thank you David but it still seems conflicting to me. V/nm and V/m are 100 > times different! If it is in V/nm then force unit should be wrong! > > On Thu, Jan 14, 2016 at 12:20 PM,

Re: [gmx-users] Electric field unit

Thank you David but it still seems conflicting to me. V/nm and V/m are 100 times different! If it is in V/nm then force unit should be wrong! On Thu, Jan 14, 2016 at 12:20 PM, mah maz wrote: > Hi David, > > In the manual 4.6.7, Page8. It seems logical since the force unit is

Re: [gmx-users] Electric field unit

On 14/01/16 08:24, mah maz wrote: Dear users, What is the electric field unit in gromacs? In the manual it is KJ/mol.nm.e but in the source code I encountered V/nm which is about 100 times KJ/mol.nm.e. V/nm. Then the manual is wrong, but where did you read that? Thank you. -- David van

Re: [gmx-users] Electric field unit

On 14/01/16 16:50, mah maz wrote: Thank you David but it still seems conflicting to me. V/nm and V/m are 100 times different! If it is in V/nm then force unit should be wrong! Did you check it yourself? From units.h: #define E_CHARGE (1.602176565e-19) #define FARADAY (E_CHARGE*AVOGADRO) /*

Re: [gmx-users] electric field

Thank you Erik and Viet Man! On Mon, Nov 16, 2015 at 6:24 PM, Man Hoang Viet wrote: > Hi, > > I can confirm electric field (even laser-pulse form) in GROMACS (all > version from 3.0 to current newest one) work fine. To check it, you may > consider a system containing only

Re: [gmx-users] electric field

Hi, I can confirm electric field (even laser-pulse form) in GROMACS (all version from 3.0 to current newest one) work fine. To check it, you may consider a system containing only an ion (say Na+) in vacuum and set mdp file as: ### dt = 0.0002; ps ! nsteps =