[gmx-users] Re: gmx-users Digest, Vol 84, Issue 217
saly jackson
saly.jackson12 at gmail.com
Thu Apr 28 19:13:26 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)
>
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> ----------------------------------------------------------------------
>
> 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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