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.
[email protected] http://folding.bmc.uu.se
--
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