[gmx-users] Fwd: gmx-users Digest, Vol 84, Issue 217

saly jackson saly.jackson12 at gmail.com
Sat Apr 30 07:21:29 CEST 2011


Hi Ivan

If in my system there are some of the other components such
SDS surfactant and one of these polarizable models can I use forcefield
parameters from PRODRG or not.
If no, would you please tell me about the references that I can find some
other components in polarizable water model
 force fields.

Thanks alot for your help

Regards

Saly
On Wed, Apr 27, 2011 at 5:29 PM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
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>   1. Re: polarizable water models (Mark Abraham)
>   2. Re: polarizable water models (Ivan Gladich)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 27 Apr 2011 22:39:56 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] polarizable water models
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DB80E9C.7010301 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 4/27/2011 10:08 PM, saly jackson wrote:
> > Hi Ivan
> >
>
> Please do not reply to whole digests with non-descriptive subject lines.
> It confuses the archives, and alienates people from finding out the
> topic of your interest, and thus being bothered to give you free help.
> Please leave only the relevant discussion, and use a useful subject line.
>
> > In which force field can I find the polarizable water models you said
> > in section "b" of your reply
>
> Have you done your own literature searching first? Then you'd already
> know what force fields they might have been used with...
>
> Mark
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 27 Apr 2011 15:43:27 +0200
> From: Ivan Gladich <ivan.gladich at marge.uochb.cas.cz>
> Subject: Re: [gmx-users] polarizable water models
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DB81D7F.70705 at marge.uochb.cas.cz>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Skipped content of type multipart/alternative-------------- next part
> --------------
> ;
> ; Topology file for SW
> ;
> ; Paul van Maaren and David van der Spoel
> ; Molecular Dynamics Simulations of Water with Novel Shell Model Potentials
> ; J. Phys. Chem. B. 105 (2618-2626), 2001
> ;
> ; Force constants for the shell are given by:
> ;
> ; k = qs^2/(4 pi eps0 alpha)
> ; However, in the current version of the itp file and software (3.2+)
> ; force constants are computed in mdrun, and the input is the
> ; polarizability in nm^3.
> ;
> ; Some data: mu (water) = 1.8546 D ( 0.0386116 e nm)
> ;            1/(4 pi eps0 alpha) = 94513.94
> ;
> ; Alpha-X = 1.415   kx = 608069
> ; Alpha-Y = 1.528   ky = 563101
> ; Alpha-Z = 1.468   kz = 586116
> ;
> ; Alpha   = 1.470   k  = 585318
> ;
> ; Bonding parameters from (but without cubic term):
> ; D. M. Ferguson:
> ; Parametrization and Evaluation of a Flexible Water Model
> ; J. Comp. Chem. 16(4), 501-511 (1995)
> ;
> ; Possible defines that you can put in your topol.top:
> ; -DANISOTROPIC Select anisotropic polarizibility (isotropic is default).
> ; -DRIGID       Rigid model (flexible is default)
> ; -DPOSRES      Position restrain oxygen atoms
> ;
>
> [ defaults ]
> LJ      Geometric
>
> [ atomtypes ]
> ;name        mass      charge   ptype   c6      c12
>   WO    15.99940       0.0     A       0.0     0.0
>   WH     1.00800       0.0     A       0.0     0.0
>   WS     0.0           0.0     S       0.0     0.0
>   WD     0.0           0.0     D       0.0     0.0
>
> [ nonbond_params ]
> #ifdef RIGID
> #ifdef ANISOTROPIC
> WH      WH      1       4.0e-5          4.0e-8
> WS      WO      1       1.0e-6          1.0e-12
> WS      WH      1       4.0e-5          2.766e-08
> WO      WO      1       2.0e-3          1.174e-06
> #else
> WH      WH      1       4.0e-5          4.0e-8
> WS      WO      1       1.0e-6          1.0e-12
> WS      WH      1       4.0e-5          2.769e-08
> WO      WO      1       2.0e-3          1.176e-06
> #endif
> #else
> #ifdef ANISOTROPIC
> WH      WH      1       4.0e-5          4.0e-8
> WS      WO      1       1.0e-6          1.0e-12
> WS      WH      1       4.0e-5          2.910e-08
> WO      WO      1       2.0e-3          1.189e-06
> #else
> WH      WH      1       4.0e-5          4.0e-8
> WS      WO      1       1.0e-6          1.0e-12
> WS      WH      1       4.0e-5          2.937e-08
> WO      WO      1       2.0e-3          1.187e-06
> #endif
> #endif
>
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ;; This is a the 'classical YAW' model, in which we do have the dummy.
> ;; The shell is attached to the dummy, in this case the gas-phase
> ;; quadrupole is correct. Water_pol routine can be used for this
> ;; model. This has four interaction sites.
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> [ moleculetype ]
> ; molname       nrexcl
> SW              2
>
> [ atoms ]
> ; id    at type res nr  residu name     at name         cg nr   charge
> 1       WO      1       SM2             OW1             1       1.24588
> 2       WH      1       SM2             HW2             1       0.62134
> 3       WH      1       SM2             HW3             1       0.62134
> 4       WD      1       SM2             DW              1       0.0
> 5       WS      1       SM2             SW              1       -2.48856
>
> #ifdef ANISOTROPIC
> [ water_polarization ]
> ; See notes above. Alphas in nm^3 (See ref. above)
> ; O H H D S funct  al_x  al_y     al_z          rOH     rHH     rOD
>  1 2 3 4 5 1   0.001415 0.001528 0.001468      0.09572 0.15139 0.0137408
>
> #else
>
> [ polarization ]
> ; See notes above.      alpha (nm^3)
> 4       5       1       0.00147
> #endif
>
> #ifdef RIGID
> [ settles ]
> ; i     funct   dOH     dHH
> 1       1       0.09572 0.15139
>
> #else
>
> [ bonds ]
> 1       2       1   0.09572     458148.
> 1       3       1   0.09572     458148.
>
> [ angles ]
> ; i     j       k
> 2       1       3    1   104.52     417.6
> #endif
>
> [ dummies3 ]
> ; The position of the dummies is computed as follows:
> ;
> ;               O
> ;
> ;               D
> ;
> ;       H               H
> ;
> ; 2 * b = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
> ;         0.0137408 nm  / [ cos (104.52 / 2 deg) * 0.09572 nm   ]
> ;         0.01557 nm
> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-X1)
> ;
> ; Dummy from                    funct   a               b
> 4       1       2       3       1       0.117265878     0.117265878
>
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1       2       3       4       5
> 2       1       3       4       5
> 3       1       2       4       5
> 4       1       2       3       5
> 5       1       2       3       4
>
> #ifdef POSRES
> ; Restrain the oxygen...
> [ position_restraints ]
> ; iatom type    fx      fy      fz
> 1       1       100     100     100
> #endif
>
> -------------- next part --------------
> ;Ivan Gladich, Prague 26/02/2011
> ; Topology file for SWM4-NDP obtained from
> ;
> ; G. Lamoureux, A. D. MacKerell, Jr., B. Roux et. al.
> ; A polarizable model of water for molecular dynamics simulations of
> biomoleculesbased on classical Drude oscillators
> ; Chem. Phys. Lett.,418,245-249, 2005
> ;
>
>
> [ defaults ]
> ;nbfunc (1=LJ,2=Buck)
> 1      2
>
> [ atomtypes ]
> ;name        mass      charge   ptype   sigma    epsilon
>   WO    15.99940       0.0     A      0.318395  0.88257296
>   WH     1.00800       0.0     A       0.0      0.0
>   WS     0.0           0.0     S       0.0      0.0
>   WD     0.0           0.0     D       0.0      0.0
>
>
> [ moleculetype ]
> ; molname       nrexcl
> SW              2
>
> [ atoms ]
> ; id    at type res nr  residu name     at name         cg nr   charge
> 1       WO      1       SM2             OW1             1       1.71636
> 2       WH      1       SM2             HW2             1       0.55733
> 3       WH      1       SM2             HW3             1       0.55733
> 4       WD      1       SM2             DW              1      -1.11466
> 5       WS      1       SM2             SW              1      -1.71636
>
> [ polarization ]
> ; See notes above.      alpha (nm^3)
> ;The drude particle is attached to the oxygen atom!!!!!
> 1       5       1       0.00097822
>
>
> [ settles ]
> ; dHH = 0.15139 gives HOH agle equal to 104.52 degree
> ; i    funct  dOH    dHH
>  1     1      0.09572       0.15139
>
> ;[ constraints ]
> ; i     funct   doh     dhh
> ;1       2       1       0.09572
> ;1       3       1       0.09572
> ;3       2       1       0.15139
>
> [ virtual_sites3 ]
> ; The position of the dummies is computed as follows:
> ;
> ;               O
> ;
> ;               D
> ;
> ;       H               H
> ; "a" and "b" are wieight
> ;the dummy 4 is in the plane of atom 1 2 3.
> ;Function 2 means that rd= rO+b(rOH1+arH1H2)/|rOH1+arH1H2|(see manual)
> ;so a=1/2 and b the distance from the oxygen atom
> ; Dummy from                    funct   a               b
> 4       1       2       3       2       0.5      0.024034
>
>
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1       2       3       4       5
> 2       1       3       4       5
> 3       1       2       4       5
> 4       1       2       3       5
> 5       1       2       3       4
>
>
> [ system ]
> Ice TIP5P-Ew T300
>
> [ molecules ]
> SW        1792
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 84, Issue 217
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