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Question of Pull Efield command
#37745 11/29/19 07:51 AM
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Dear Charmm users,

I am studying the motion of a simple polar molecule with overall zero charge under electric field using drude polarizable model and forcefield. I calculated the dipole moment of molecule and applied E-field at direction of dipolemoment using 'Pull Efield command'. Then, I ran a NPT simulation to equilibrate the system under electric field. But, I found displacement of center of mass of the molecule were exactly same under different strength electric field. This does not make sense to me, since in Drude model, atoms are assigned partial charges and should feel Coloumbic interaction from E field. The following is how I set up simulation. Any thoughts and commands are very appreciated. Thank you.

! load Drude rtf/forcefield
stream drude_protein/model.str
! load molecule psf, crd, restart file
open read unit 10 card name mole.psf
read psf unit 10 card
...
! print initial coordinates of atoms
SCALar charge show
scalar x show
scalar y show
scalar z show
!set up crystal and image
crystal define/read ...
image BYSEgments xcen...
!set up non bond interaction
update inbfrq -1 imgfrq -1 ihbfrq 0 -
ewald pmewald kappa 0.34 fftx 32 ffty 32 fftz 32 order 6 lrc -
! apply E-field
set approxfield 1E5 ! units of V/m
coor dipole select all end
pull efield @approxfield xdir ?xdip ydir ?ydip zdir ?zdip
! equilibration by NPT
TPCONTROL NTHER 2 CMDAMP 10.0 NSTEP 20 -
THER 1 TAU 0.1 TREF @temp SELECT .NOT. TYPE D* END -
THER 2 TAU 0.005 TREF 1.00 SELECT TYPE D* END -
BARO BTAU 0.2 PREF 1.00 DSCY
SHAKE bonh param tolerance 1.0e-9 -
nofast -
select ( .not. (type D*)) end -
select ( .not. (type D*)) end noreset

drudehardwall l_wall 0.2

DYNAMICS vv2 start nstep 100000 timestp 0.001 -
ntrfrq 5000 iprfrq -1 -
nprint 1000 iseed @seed -
iasvel 1 firstt @temp finalt @temp -
inbfrq -1 imgfrq -1 ihbfrq 0 ilbfrq 0 -
iunread 91 Kunit 70 -
iunwrite 93 -
iuncrd 92 nsavcrd 1000

! turn off the e-field
pull off
! Print coordinates
scalar x show
scalar y show
scalar z show

By changing @approxfield, x, y ,z of molecules did not change at all.

Last edited by Allen_123; 11/29/19 07:53 AM.
Re: Question of Pull Efield command
Allen_123 #37751 11/29/19 04:43 PM
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What happens if you do the same with an additive (non-Drude) model of the same molecule?


Rick Venable
computational chemist

Re: Question of Pull Efield command
Allen_123 #37763 12/03/19 04:29 AM
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Dear Dr.Venable

I'm still doing the simulation with non-drude charmm36 forcefield. Most likely, Charmm36 will also provide negative result, but might due to different reason that Charmm does not assign partial charges to atoms. I just checked the Drude simulation output again. The energy and lattice parameter are also exactly same at every step with or without electric field. Is it possible that I did not invoke "pull efield" correctly?

Thank you.

Re: Question of Pull Efield command
Allen_123 #37764 12/03/19 05:04 PM
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I'm not sure, as I have limited experience with EFIELD myself, and have never used it with the VV2 integrator or with Drude. You may need to devise some more detailed tests of simple systems and examine the forces.


Rick Venable
computational chemist

Re: Question of Pull Efield command
Allen_123 #37765 12/03/19 08:58 PM
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I agree with Rick. Science is not about asking questions on various internet forums. A good way to learn is to perform small experiments in order to either narrow down a problem or to understand how something actually works.
For instance regarding this particular problem - is it the DRUDE forcefield, the integrator, the EFIEld option to the PULL command? All these are very easy to test with a very small system.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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