[gmx-users] SWM4-NDP force field

[Dr. Vitaly Chaban]

The assigned masses are due to the presence of dummy atoms. The model
molecule must represent moments of inertia.

1-4 (fudgeLJ and fudgeQQ) interactions do not apply for water. So, you care
about a larger molecule only.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН




On Sat, Oct 18, 2014 at 8:39 AM, Kester Wong <Kester2014 at ibs.re.kr> wrote:
>
> Dear all,
>
>
>
> I would like to know if this would cause a difference in MD calculations
(text highlighted in red):
>
> The assigned mass for the hydroxide O-atom seems to be inconsistent. Was
the zero atomic mass set with a specific purpose?
>
>
> #define SHELLPTYPE S
>
> #define SHELLMASS  0
>
> #define OXYGENMASS 15.9994
>
>
> [ atomtypes ]
>
> ; name          btype   mass    charge   ptype     sigma        epsilon
>
>  SWM4-NDP_110a  OD    SHELLMASS    -1.71636    SHELLPTYPE      0.0
   0.0
>
>  SWM4-NDP_OV1   OV1     1.0            0.0     A       0.24
0.294191
>
>  SWM4-NDP_OV2   OV2     0.0            0.0     D       0.28
0.294191
>
>  SWM4-NDP_H     H       1.008          0.0     A       0.07
0.294191
>
>  SWM4-NDP_qH    qH      0.0           0.23     D       0.0          0.0
>
>  SWM4-NDP_O     O       0.0          0.203     A       0.0          0.0
>
>
>
> ; Hydroxide
>
> [ moleculetype ]
>
> ; molname       nrexcl
>
> OH-            2
>
>
> [ atoms ]
>
> ; id    at type res nr  residu name     at name      cg nr   charge   mass
>
>  1    SWM4-NDP_O       1       OH-               O     1       0.202
 11.998
>
>  2    SWM4-NDP_110a    1       OH-              OS     1      -1.432
0.00
>
>  3    SWM4-NDP_H       1       OH-               H     1       0.00
 1.008
>
>  4    SWM4-NDP_OV1     1       OH-             OV1     1       0.00    1.0
>
>  5    SWM4-NDP_OV1     1       OH-             OV1     1       0.00    1.0
>
>  6    SWM4-NDP_OV1     1       OH-             OV1     1       0.00    1.0
>
>  7    SWM4-NDP_OV1     1       OH-             OV1     1       0.00    1.0
>
>  8    SWM4-NDP_OV2     1       OH-             OV2     1       0.00
 0.00
>
>  9    SWM4-NDP_qH      1       OH-              qH     1       0.23
 0.00
>
>
> [ polarization ]
>
> #ifdef POL2WATER
>
> 1     2     2  0.0006809        0.02   16.736e8
>
> #else
>
> 1     2     1  0.0006809
>
> #endif
>
>
> ; Initialy developed as a harmonic bond
>
> ; Conversion: alpha=sqrt(qS)/(4*pi*eps0*CAL2J*A2NM*k) =  138.9354492 *
sqrt(qS)/k
>
> ; [ bonds ]
>
> ; 1 2 6 0.0 418400
>
>
> [ constraints ]
>
>  3 1 1 0.0968
>
>  4 1 1 0.1463
>
>  5 1 1 0.1463
>
>  6 1 1 0.1463
>
>  7 1 1 0.1463
>
>  4 6 1 0.1979
>
>  6 5 1 0.1979
>
>  5 7 1 0.1979
>
>  7 4 1 0.1979
>
>
> #ifdef CONSTRAINTS
>
> [ constraints ]
>
>  3 4 1 0.15
>
>  3 5 1 0.15
>
>  3 6 1 0.15
>
> ; A fourth constraint would make the system redundant and therefore
>
> ; numerically unstable.
>
> ; 3 7 1 0.15
>
> #else
>
> [ angles ]
>
>  3 1 4 1 73.11         683
>
>  3 1 5 1 73.11         683
>
>  3 1 6 1 73.11         683
>
>  3 1 7 1 73.11         683
>
> #endif
>
>
> [ dummies2 ]
>
>     8     3     1     1    1.4390
>
>     9     3     1     1   -0.3099
>
>
> [ exclusions ]
>
>  1 2 3 4 5 6 7 8 9
>
>  2 1 3 4 5 6 7 8 9
>
>  3 1 2 4 5 6 7 8 9
>
>  4 1 2 3 5 6 7 8 9
>
>  5 1 2 3 4 6 7 8 9
>
>  6 1 2 3 4 5 7 8 9
>
>  7 1 2 3 4 5 6 8 9
>
>  8 1 2 3 4 5 6 7 9
>
>  9 1 2 3 4 5 6 7 8
>
>
>
> If I am to add/define graphene's bonded and nonbonded parameters into the
SWM4-NDP force field, using CHARMM27 parameters, should I take into
consideration the fudgeLJ and fudgeQQ differences (0.5 fudge LJ and fudgeQQ
in SWM4-NDP, 1.0 for fudgeLJ and fudgeQQ in CHARMM27)? The comb-rules are
the same (no.2).
>
>
>
> Thanks in advance!
>
> Kester