[gmx-users] SWM4-NDP force field

Dr. Vitaly Chaban vvchaban at gmail.com
Mon Oct 20 07:24:20 CEST 2014


Hi Kester -

The four dummy atoms carry a mass of 1 a.m.u each, hence the oxygen mass of
11.998.

However, what I don't understand is that the same atom has a mass of 0.0
under [ atomtypes ].

-- The later section overwrites previous one, so it is possible to write
zeros for charges and masses in [atomtypes] if you then write correct
numbers in [atoms]. I believe this situation is due to historical reasons.

For a system consisting of graphene, water and (Na+ OH-, or H3O+ Cl-) ions,
if there is nonbonding-parameters specified, will having a different fudge
value (0.5 instead of 1.0) make a difference?

-- Yes, it will -- but only for graphene. Small particles do not exhibit
1-4 interactions, because they do NOT possess atoms which are separated by
3 covalent bonds, -C-C-C-C-.

1-4 interactions work as a supplement to the dihedral function. To
understand which number (0.5 or 1.0 or what you like) works better, you
will have to compare dihedrals from MD simulations with those you expect
(from X-ray structure, from electronic structure description, etc).
Normally, 1-4 interactions do matter, but they don't make a global
difference.

Best of luck,
Vitaly

Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН




On Mon, Oct 20, 2014 at 6:13 AM, Kester Wong <Kester2014 at ibs.re.kr> wrote:

> Hi Dr. Chaban,
>
>
> The four dummy atoms carry a mass of 1 a.m.u each, hence the oxygen mass
> of 11.998.
>
> However, what I don't understand is that the same atom has a mass of 0.0
> under [ atomtypes ].
>
>
> For a system consisting of graphene, water and (Na+ OH-, or H3O+ Cl-)
> ions, if there is nonbonding-parameters specified, will having a different
> fudge value (0.5 instead of 1.0) make a difference?
>
>
> Thank you in advance.
>
>
> Regards,
>
> Kester
> --------- 원본 메일 ---------
>
> *보낸사람* : "Dr. Vitaly Chaban" <vvchaban at gmail.com>
> *받는사람* : <gmx-users at gromacs.org>
> *받은날짜* : 2014년 10월 18일(토) 16:20:49
> *제목* : Re: [gmx-users] SWM4-NDP force field
>
> 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  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
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