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

[Erik Marklund]

Dear Ivan,

It works also without PME and for non-neutral systems. What are your COM-removal settings? They can certainly mess up an accelerating system.

Kind regards,
Erik

> On 10 Mar 2016, at 10:33, Ivan Gladich <igladich at sissa.it> wrote:
> 
> Dear Prof. Spoel
> first of all thank you for your reply.
> 
> 1) No, I did not get any warning about PME and charge system, just a note
> 
> NOTE 4 [file topol.top, line 23]:
>  System has non-zero total charge: 1.000000
>  Total charge should normally be an integer. See
>  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>  for discussion on how close it should be to an integer
> 
> 
> 2) I tried the simulation with a plain cut-off scheme and no PME and but still my positive ion moves with constant velocity.
> At the link below you can see my files, the coord.xvg and the veloc.xvg for the coordinates and the velocity of my ion
> 
> https://goo.gl/Q0pyR9
> 
> 3) Following your suggestions, I have also tried an MD using PME and two ions of opposite charge. The two ions were placed at about 2.5 nm distance, interacting only through electrostatic and with a cut-off of 0.9 nm. Interestingly, here the behavior seems correct with the velocity that grows linearly with time (see velocBr.xvg and velocNa.xvg attached in the link below)
> 
> https://goo.gl/TDM0lZ
> 
> Thus  my new  question....Does the electric field in Gromacs works only with PME and neutral system?
> 
> Thank you very very much for your help
> Ivan
> 
> 
> On 2016-03-09 20:10, David van der Spoel wrote:
>> 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
> 
> -- 
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