[gmx-users] Shell molecular dynamics
David
spoel at xray.bmc.uu.se
Thu Mar 20 19:36:18 CET 2003
On Thu, 2003-03-20 at 15:43, Martin Mucha wrote:
> Hi all,
>
> I would like to use polarizability model in my simulations,
> but I do not know how. There are several paragraphs about the topic in the
> manual, however
> I did not find any mention about how to actually tell gromacs that I am using
> the shell model, e.g. How to set up topology, mdp and gro files. I would be
> grateful for any idea, or sample input files of a working shell MD.
see attached itp file for our polarizable water model. This is not a
perfect model! See JPCB 105 (2001) 2618-2626
You can use the mkyaw program in contrib to transform an SPC water box
into a SW box.
>
> Martin Mucha
>
>
> --
> address: UFCH JH AV CR, m. 224
> Dolejskova 3, 18223 Praha 8, Czech Republic
> tel: +420266053495, +420736175269
> -----------------------------------------------------
>
>
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--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------- 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)
;
; 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:
; -DANISOTROPIC Select anisotropic polarizibility.
; -DRIGID Rigid model (flexible is default)
; -DPOSRES Position restrain oxygen atoms
;
[ defaults ]
LJ Arithmetic
[ 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
[ position_restraints ]
; See notes above.
; i funct kx ky kz rOH rHH rOD
#ifdef ANISOTROPIC
1 2 608069 563101 586116 0.09572 0.15139 0.0137408
#else
1 2 585318 585318 585318 0.09572 0.15139 0.0137408
#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
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