[gmx-users] Query about a simple MD with constant electric field
Ivan Gladich
igladich at sissa.it
Mon Mar 14 13:30:44 CET 2016
Dear Erik,
yes, that was the problem.
I set
comm-mode = none
and now it works also without PME and for non-neutral systems
Thank you very much
Ivan
On 2016-03-14 10:50, Erik Marklund wrote:
> 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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