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Dear Saly<br>
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.<br>
<br>
You can try to find something in literature but I have the
impression that nobody has tested SDS with these water models.<br>
As I told you in the previous mail these water models are quite
recent.<br>
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.<br>
Good luck<br>
Ivan<br>
<br>
<br>
On 04/30/2011 07:21 AM, saly jackson wrote:
<blockquote
cite="mid:BANLkTim6nicAm+PaMTzc=2zgtZhN8WUi5g@mail.gmail.com"
type="cite"><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 class="h5">
<div class="gmail_quote">On Wed, Apr 27, 2011 at 5:29 PM, <span
dir="ltr"><<a moz-do-not-send="true"
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wrote:<br>
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Today's Topics:<br>
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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 moz-do-not-send="true"
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
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href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
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<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 moz-do-not-send="true"
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
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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>
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End of gmx-users Digest, Vol 84, Issue 217<br>
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</font></blockquote>
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<br>
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</div>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
------
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: <a class="moz-txt-link-abbreviated" href="mailto:ivan.gladich@uochb.cas.cz">ivan.gladich@uochb.cas.cz</a>
web page:<a class="moz-txt-link-freetext" href="http://www.molecular.cz/~gladich/">http://www.molecular.cz/~gladich/</a>
-----</pre>
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