[gmx-users] Query about a simple MD with constant electric field

[David van der Spoel]

On 09/03/16 11:48, Ivan Gladich wrote:
> Dear Gromacs users
>
> I am doing a very simple MD with a constant electric field of 1 V/nm
> along the positive z-direction in a system containing only one Na+ ion,
> starting from rest.
> The ion is not coupled to the thermostat and it is placed in a box of 4
> nm* 4nm * 16 nm, in the X,Y,and Z direction respectively.
>
>   I would expect my ion accelerating along the positive Z-direction with
> constant acceleration.
> However my ion  starts to move in the positive  Z-direction but with
> constant velocity for all my 1 ns MD. Do I do something really wrong?
>
Yes :).
I guess you got at least a warning from grompp, right? About using a 
charged system with PME. If you have a net charge in the system PME 
compensates for it by applying a homogeneous charge distribution with 
the opposite sign. This can give interesting results.
You could try using a cut-off instead if you just have one particle. Or 
use an ion pair.

> I am using gromacs 5.1.1 in double precision
>
> Thanks for any possible help
> Below my inputs
> Ivan
>
> ###########
> conf.gro
> ###########
>
> Gyas ROwers Mature At Cryogenic Speed
>   1
>   2183Na      Na 6545   3.014   0.540   8.909
>     4.00000   4.00000  16.00000
>
> ##########
> topol.top
> #########
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               2               yes             0.5     0.8333
>
> [ atomtypes ]
> ;name  at.num   mass       charge   ptype   sigma   epsilon
> Na        11      79.90    1.0000  A    0.385       0.0022
>
> [ moleculetype ]
> ; molname       nrexcl
> Na              1
>
> [ atoms ]
> ; id    at type         res nr  residu name     at name  cg nr  charge
> 1       Na              1       Na              Na       1      1.00000
>
> [ system ]
>   THE-BEST
>
> [ molecules ]
> ; Compound        nmols
>   Na              1
>
>
> #########
> grompp.mdp
> #########
>
> title       = Na+Electric
>
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 1000000   ;  = 1000ps
> dt          = 0.001     ; 1 fs
>
> ; Output control
> nstxout     = 0       ; save coordinates every 1.0 ps
> nstvout     = 1000       ; save velocities every 1.0 ps
> nstenergy   = 5000    ; save energies every 1 ps
> nstlog      = 5000    ; update log file every 1 ps
> nstxtcout   = 1000    ; xtc compressed trajectory output every 1 ps
>
> ; Neighborsearching
> cutoff-scheme   = group ;Verlet
> ns_type         = grid      ; search neighboring grid cells
> nstlist         = 1        ; 20 fs, largely irrelevant with Verlet
> rlist           = 0.9
> rcoulomb        = 0.9       ; short-range electrostatic cutoff (in nm)
> rvdw            = 0.9       ; short-range van der Waals cutoff (in nm)
>
> ; Electrostatics
> coulombtype     = PME       ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4         ; cubic interpolation
> fourierspacing  = 0.16      ; grid spacing for FFT
>
> ; Temperature coupling
> tcoupl      = no ;
>
> ; Pressure coupling
> pcoupl      = no;
>
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
>
> ; Dispersion correction
> DispCorr    = no ;
>
> ; Velocity generation
> gen_vel     = no
>
> ;Electric
>
> E-x = 0 0 0
> E-y = 0 0 0
> E-z = 1 1 0 : 1 V nm-1
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se