<br><div class="gmail_quote"><div>Hi Ivan </div>
<div> </div>
<div>If in my system there are some of the other components such <br>SDS surfactant and one of these polarizable models can I use forcefield parameters from PRODRG or not.</div>
<div>If no, would you please tell me about the references that I can find some other components in polarizable water model</div>
<div> force fields.</div>
<div> </div>
<div>Thanks alot for your help </div>
<div> </div>
<div>Regards</div>
<div> </div><font color="#888888">
<div>Saly<br></div></font><div><div></div><div class="h5">
<div class="gmail_quote">On Wed, Apr 27, 2011 at 5:29 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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<br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. Re: polarizable water models (Mark Abraham)<br> 2. Re: polarizable water models (Ivan Gladich)<br>
<br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Wed, 27 Apr 2011 22:39:56 +1000<br>From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] polarizable water models<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4DB80E9C.7010301@anu.edu.au" target="_blank">4DB80E9C.7010301@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>On 4/27/2011 10:08 PM, saly jackson wrote:<br>> Hi Ivan<br>><br><br>Please do not reply to whole digests with non-descriptive subject lines.<br>It confuses the archives, and alienates people from finding out the<br>
topic of your interest, and thus being bothered to give you free help.<br>Please leave only the relevant discussion, and use a useful subject line.<br><br>> In which force field can I find the polarizable water models you said<br>
> in section "b" of your reply<br><br>Have you done your own literature searching first? Then you'd already<br>know what force fields they might have been used with...<br><br>Mark<br><br><br><br><br><br>
------------------------------<br>
<br>Message: 2<br>Date: Wed, 27 Apr 2011 15:43:27 +0200<br>From: Ivan Gladich <<a href="mailto:ivan.gladich@marge.uochb.cas.cz" target="_blank">ivan.gladich@marge.uochb.cas.cz</a>><br>Subject: Re: [gmx-users] polarizable water models<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4DB81D7F.70705@marge.uochb.cas.cz" target="_blank">4DB81D7F.70705@marge.uochb.cas.cz</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br><br>Skipped content of type multipart/alternative-------------- next part --------------<br>;<br>; Topology file for SW<br>;<br>; Paul van Maaren and David van der Spoel<br>
; Molecular Dynamics Simulations of Water with Novel Shell Model Potentials<br>; J. Phys. Chem. B. 105 (2618-2626), 2001<br>;<br>; Force constants for the shell are given by:<br>;<br>; k = qs^2/(4 pi eps0 alpha)<br>; However, in the current version of the itp file and software (3.2+)<br>
; force constants are computed in mdrun, and the input is the<br>; polarizability in nm^3.<br>;<br>; Some data: mu (water) = 1.8546 D ( 0.0386116 e nm)<br>; 1/(4 pi eps0 alpha) = 94513.94<br>;<br>; Alpha-X = 1.415 kx = 608069<br>
; Alpha-Y = 1.528 ky = 563101<br>; Alpha-Z = 1.468 kz = 586116<br>;<br>; Alpha = 1.470 k = 585318<br>;<br>; Bonding parameters from (but without cubic term):<br>; D. M. Ferguson:<br>; Parametrization and Evaluation of a Flexible Water Model<br>
; J. Comp. Chem. 16(4), 501-511 (1995)<br>;<br>; Possible defines that you can put in your topol.top:<br>; -DANISOTROPIC Select anisotropic polarizibility (isotropic is default).<br>; -DRIGID Rigid model (flexible is default)<br>
; -DPOSRES Position restrain oxygen atoms<br>;<br><br>[ defaults ]<br>LJ Geometric<br><br>[ atomtypes ]<br>;name mass charge ptype c6 c12<br> WO 15.99940 0.0 A 0.0 0.0<br>
WH 1.00800 0.0 A 0.0 0.0<br> WS 0.0 0.0 S 0.0 0.0<br> WD 0.0 0.0 D 0.0 0.0<br><br>[ nonbond_params ]<br>#ifdef RIGID<br>#ifdef ANISOTROPIC<br>
WH WH 1 4.0e-5 4.0e-8<br>WS WO 1 1.0e-6 1.0e-12<br>WS WH 1 4.0e-5 2.766e-08<br>WO WO 1 2.0e-3 1.174e-06<br>#else<br>WH WH 1 4.0e-5 4.0e-8<br>
WS WO 1 1.0e-6 1.0e-12<br>WS WH 1 4.0e-5 2.769e-08<br>WO WO 1 2.0e-3 1.176e-06<br>#endif<br>#else<br>#ifdef ANISOTROPIC<br>WH WH 1 4.0e-5 4.0e-8<br>
WS WO 1 1.0e-6 1.0e-12<br>WS WH 1 4.0e-5 2.910e-08<br>WO WO 1 2.0e-3 1.189e-06<br>#else<br>WH WH 1 4.0e-5 4.0e-8<br>WS WO 1 1.0e-6 1.0e-12<br>
WS WH 1 4.0e-5 2.937e-08<br>WO WO 1 2.0e-3 1.187e-06<br>#endif<br>#endif<br><br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>;; This is a the 'classical YAW' model, in which we do have the dummy.<br>
;; The shell is attached to the dummy, in this case the gas-phase<br>;; quadrupole is correct. Water_pol routine can be used for this<br>;; model. This has four interaction sites.<br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
[ moleculetype ]<br>; molname nrexcl<br>SW 2<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge<br>1 WO 1 SM2 OW1 1 1.24588<br>
2 WH 1 SM2 HW2 1 0.62134<br>3 WH 1 SM2 HW3 1 0.62134<br>4 WD 1 SM2 DW 1 0.0<br>
5 WS 1 SM2 SW 1 -2.48856<br><br>#ifdef ANISOTROPIC<br>[ water_polarization ]<br>; See notes above. Alphas in nm^3 (See ref. above)<br>; O H H D S funct al_x al_y al_z rOH rHH rOD<br>
1 2 3 4 5 1 0.001415 0.001528 0.001468 0.09572 0.15139 0.0137408<br><br>#else<br><br>[ polarization ]<br>; See notes above. alpha (nm^3)<br>4 5 1 0.00147<br>#endif<br><br>#ifdef RIGID<br>[ settles ]<br>
; i funct dOH dHH<br>1 1 0.09572 0.15139<br><br>#else<br><br>[ bonds ]<br>1 2 1 0.09572 458148.<br>1 3 1 0.09572 458148.<br><br>[ angles ]<br>; i j k<br>
2 1 3 1 104.52 417.6<br>#endif<br><br>[ dummies3 ]<br>; The position of the dummies is computed as follows:<br>;<br>; O<br>;<br>; D<br>;<br>; H H<br>;<br>
; 2 * b = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]<br>; 0.0137408 nm / [ cos (104.52 / 2 deg) * 0.09572 nm ]<br>; 0.01557 nm<br>; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-X1)<br>;<br>; Dummy from funct a b<br>
4 1 2 3 1 0.117265878 0.117265878<br><br>[ exclusions ]<br>; iatom excluded from interaction with i<br>1 2 3 4 5<br>2 1 3 4 5<br>3 1 2 4 5<br>
4 1 2 3 5<br>5 1 2 3 4<br><br>#ifdef POSRES<br>; Restrain the oxygen...<br>[ position_restraints ]<br>; iatom type fx fy fz<br>1 1 100 100 100<br>
#endif<br><br>-------------- next part --------------<br>;Ivan Gladich, Prague 26/02/2011<br>; Topology file for SWM4-NDP obtained from<br>;<br>; G. Lamoureux, A. D. MacKerell, Jr., B. Roux et. al.<br>; A polarizable model of water for molecular dynamics simulations of biomoleculesbased on classical Drude oscillators<br>
; Chem. Phys. Lett.,418,245-249, 2005<br>;<br><br><br>[ defaults ]<br>;nbfunc (1=LJ,2=Buck)<br>1 2<br><br>[ atomtypes ]<br>;name mass charge ptype sigma epsilon<br> WO 15.99940 0.0 A 0.318395 0.88257296<br>
WH 1.00800 0.0 A 0.0 0.0<br> WS 0.0 0.0 S 0.0 0.0<br> WD 0.0 0.0 D 0.0 0.0<br><br><br>[ moleculetype ]<br>; molname nrexcl<br>SW 2<br>
<br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge<br>1 WO 1 SM2 OW1 1 1.71636<br>2 WH 1 SM2 HW2 1 0.55733<br>
3 WH 1 SM2 HW3 1 0.55733<br>4 WD 1 SM2 DW 1 -1.11466<br>5 WS 1 SM2 SW 1 -1.71636<br>
<br>[ polarization ]<br>; See notes above. alpha (nm^3)<br>;The drude particle is attached to the oxygen atom!!!!!<br>1 5 1 0.00097822<br><br><br>[ settles ]<br>; dHH = 0.15139 gives HOH agle equal to 104.52 degree<br>
; i funct dOH dHH<br> 1 1 0.09572 0.15139<br><br>;[ constraints ]<br>; i funct doh dhh<br>;1 2 1 0.09572<br>;1 3 1 0.09572<br>;3 2 1 0.15139<br>
<br>[ virtual_sites3 ]<br>; The position of the dummies is computed as follows:<br>;<br>; O<br>;<br>; D<br>;<br>; H H<br>; "a" and "b" are wieight<br>;the dummy 4 is in the plane of atom 1 2 3.<br>
;Function 2 means that rd= rO+b(rOH1+arH1H2)/|rOH1+arH1H2|(see manual)<br>;so a=1/2 and b the distance from the oxygen atom<br>; Dummy from funct a b<br>4 1 2 3 2 0.5 0.024034<br>
<br><br>[ exclusions ]<br>; iatom excluded from interaction with i<br>1 2 3 4 5<br>2 1 3 4 5<br>3 1 2 4 5<br>4 1 2 3 5<br>5 1 2 3 4<br>
<br><br>[ system ]<br>Ice TIP5P-Ew T300<br><br>[ molecules ]<br>SW 1792<br><br>------------------------------<br><font color="#888888"><br>--<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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