Dear GMX users: I want to simulate water with polarizable water molecule models? I am not clear about how to construct the itp files for them. I have seen swm-dp.itp on http://lists.gromacs.org/pipermail/gmx-users/2006-August/023476.html ; ; Topology file for SSWM4-DP ; ; G. Lamoureux, A. D. MacKerell, Jr., B. Roux ; A simple polarizable model of water based on classical Drude oscillators ; J. Chem. Phys., 119 (5185-5197), 2003 ; ; Possible defines that you can put in your topol.top: ; -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 ] WO WO 1 3.561658e-03 3.685198e-06 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ;; 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 -1.77185 2 WH 1 SM2 HW2 1 0.55370 3 WH 1 SM2 HW3 1 0.55370 4 WD 1 SM2 DW 1 -1.10740 5 WS 1 SM2 SW 1 1.77185 [ polarization ] ; See notes above. alpha (nm^3) 1 5 1 0.00104252 ;[ settles ] ; i funct dOH dHH ;1 1 0.1 0.16333 [ constraints ] ; i funct doh dhh 1 2 1 0.09572 1 3 1 0.09572 3 2 1 0.15139 [ 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 0.2031807494 0.2031807494 [ 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 But I think: [ constraints ] ; i funct doh dhh 1 2 1 0.09572 1 3 1 0.09572 3 2 1 0.15139 conflict with ;[ settles ] ; i funct dOH dHH ;1 1 0.1 0.16333 I think it should use ;[ settles ] ; i funct dOH dHH ;1 1 0.09572 0.15139 Anybody could give some helps? Thanks a lot!!! Zhongjin He
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
