[gmx-users] How can I check external electric field was applied?
koki0724 at naver.com
Sat Feb 24 04:21:21 CET 2018
Thank you Dan,
I used two graphene sheets with freeze and one sodium ion and one chloride ion are between them.
It also had same ‘gmx potential’ result when simulated without graphene sheets.
I’m now using Gromacs 5.1.4, using PME for Ewald summation with NVE ensemble for this test system.
After finishing electric field test, I’m going to use following MDP for my original system.
define = -DPOSRES_GRA -DPOSRES_CNT
t_couple = berendsen
tc_grps = GRA CNT SOL NA CL
tau_t = 0.1 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300 300
p_couple = Parrinello-Rahman
pcoupletype = semiisotropic
tau_p = 0.1
compressibility = 4.5e-5
ref_p = 1.0
constraints = none
constraint-algorithm = Lincs
E_z = 1 1 0
There is no gmx grompp error with this mdp, I just wonder the applied external e field is 1V.
Thank you, Regards :)
From: "Dan Gil"<dan.gil9973 at gmail.com>
To: <gmx-users at gromacs.org>, "이연경"<koki0724 at naver.com>
Sent: 2018. 2. 24 AM 2:36:06
Subject: Re: [gmx-users] How can I check external electric field was applied?
You guessed correctly - gmx potential only calculates the electric field and potential of the system. It does not take into account the applied field.
Are you using walls in your system? If so, are you using the 3DC correction along with PME for Ewald summation? If you answered yes to both of these question, you need to use Gromacs version 2016.4 and forwards - there has been an important bug fix.
As long as your gmx grompp didn't return any warning or errors, I would expect it to be valid. You can share your MDP file with us and that might help.
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