[gmx-users] Re: polarizable water models
Ivan Gladich
ivan.gladich at marge.uochb.cas.cz
Mon May 2 11:09:52 CEST 2011
Dear Saly
I am sorry but I am not able to help you on this because I do not
have any experience with PRODRG and SDS surfactants.
You can try to find something in literature but I have the impression
that nobody has tested SDS with these water models.
As I told you in the previous mail these water models are quite recent.
You have to test the behaviour of your SDS in these water model using
some experimental target (e.g. diffusivity, free energy of solvation or
other...) and see if the force field is reasonable.
Good luck
Ivan
On 04/30/2011 07:21 AM, saly jackson wrote:
>
> 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
> <mailto: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
> <mailto:Mark.Abraham at anu.edu.au>>
> Subject: Re: [gmx-users] polarizable water models
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4DB80E9C.7010301 at anu.edu.au
> <mailto: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
> <mailto: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
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4DB81D7F.70705 at marge.uochb.cas.cz
> <mailto: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
> ******************************************
>
>
>
--
------
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic
Tel: +420775504164
e-mail: ivan.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-----
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