Luciano Costa wrote:
Hi all and Spoel
Based on mailing list answer at Mar 20th 2003, which discribed the
entire topology file for water shell model, referencing on J. Phys. Chem
B. 105 (2618) 2001, I have tryed to run water polarization MD with this
file.itp. However, running grompp a message "Water polarization should
now be listed under [ water_polarization ]" appears. In my *.top file I
wrote:
#include "shell.itp"
[ system ]
Water
[ molecules ]
SW 500
And shell.itp is the same as reported in the cited mailing list. An
additional message was: "Source code file: topdirs.c, line: 145". At
this line, in source code, I was able to see that this error probably
comes from POSRES defintion. As can be seen below:
switch (type) {
case 1:
return F_POSRES;
case 2:
gmx_fatal(FARGS,"Water polarization should now be listed under [
water_polarization ]\n");
default:
gmx_fatal(FARGS,"Invalid position restraint type %d",type);
}
Can anyone help me to solve this problem?
see attach, the itp file is also in your share/gromacs/top directory
(i.e. $GMXLIB). Note that there are newer models from the Roux and van
Gunsteren groups that work in gromacs as well, and that you should
consider for your work.
regards
Luciano
--
### Luciano Tavares da Costa ###
Laboratory of Molecular Spectroscopy
## IQ - University of Sao Paulo - Brazil ##
http://lem.iq.usp.br;[EMAIL PROTECTED]
<http://lem.iq.usp.br;[EMAIL PROTECTED]> ##################################
------------------------------------------------------------------------
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
;
; 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
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