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-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 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.abra...@anu.edu.au> > Subject: Re: [gmx-users] polarizable water models > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4db80e9c.7010...@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.glad...@marge.uochb.cas.cz> > Subject: Re: [gmx-users] polarizable water models > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4db81d7f.70...@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 > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 84, Issue 217 > ****************************************** >
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