[gmx-users] Query about a simple MD with constant electric field
erik.marklund at chem.ox.ac.uk
Mon Mar 14 10:50:43 CET 2016
It works also without PME and for non-neutral systems. What are your COM-removal settings? They can certainly mess up an accelerating system.
> 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
> 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
> 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)
> 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
> 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
>>> Gyas ROwers Mature At Cryogenic Speed
>>> 2183Na Na 6545 3.014 0.540 8.909
>>> 4.00000 4.00000 16.00000
>>> [ 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 ]
>>> [ molecules ]
>>> ; Compound nmols
>>> Na 1
>>> 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
>>> 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
>>> 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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