[gmx-users] SWM4-NDP WATER MODEL AND IONS
D.G. Sprous, PhD
dsprous at bioleap.com
Fri Aug 12 16:22:28 CEST 2011
I am quite interested in seeing this functional in GROMACS. You appear
to have been more successful than me so far. However, I believe from
reading the papers that the Drude particle (OD_swm4ndp) should have a
mass of 0.40 while the oxygen should have a mass of 15.59994 (the true O
mass is redistributed between the Drude and the O). Further, the Drude
is movable and is not a dummy. It should be tethered to the O with a
1000 kcal/mol/angstrom bond (which I do not notice in the top file).
Comments?
On 8/12/2011 9:56 AM, zhongjin wrote:
> Dear GMX users,
> I am using GMX4.5.4 to simulate SWM4-NDP polarizable water
> model, it is OK. But when I use the ions polarizable model which is in
> conjuction with SWM4-NDP model, the *RMS force is very large:*
> step 16: EM did not converge in 20 iterations, RMS force 7.950
> step 17: EM did not converge in 20 iterations, RMS force 61.192
> step 18: EM did not converge in 20 iterations, RMS force 177.091
> step 19: EM did not converge in 20 iterations, RMS force 371.756
> step 20: EM did not converge in 20 iterations, RMS force 624.178
> step 21: EM did not converge in 20 iterations, RMS force 849.728
> step 22: EM did not converge in 20 iterations, RMS force 891.695
> step 23: EM did not converge in 20 iterations, RMS force 830.527
> step 24: EM did not converge in 20 iterations, RMS force 803.412
> step 25: EM did not converge in 20 iterations, RMS force 882.106
> step 26: EM did not converge in 20 iterations, RMS force 1031.051
> step 27: EM did not converge in 20 iterations, RMS force 1339.648
> step 28: EM did not converge in 20 iterations, RMS force 1727.688
> step 29: EM did not converge in 20 iterations, RMS force 1750.876
> step 30: EM did not converge in 20 iterations, RMS force 1445.519
> step 31: EM did not converge in 20 iterations, RMS force 0.033
> step 32: EM did not converge in 20 iterations, RMS force 1210.740
> step 33: EM did not converge in 20 iterations, RMS force 526.515
> step 34: EM did not converge in 20 iterations, RMS force 0.033
> step 35: EM did not converge in 20 iterations, RMS force 0.032
> step 36: EM did not converge in 20 iterations, RMS force 0.032
> step 37: EM did not converge in 20 iterations, RMS force 0.033
> step 38: EM did not converge in 20 iterations, RMS force 0.032
> step 39: EM did not converge in 20 iterations, RMS force 0.031
> step 40: EM did not converge in 20 iterations, RMS force 0.032
> step 41: EM did not converge in 20 iterations, RMS force 0.032
> step 42: EM did not converge in 20 iterations, RMS force 0.032
> step 43: EM did not converge in 20 iterations, RMS force 0.032
> step 44: EM did not converge in 20 iterations, RMS force 0.032
> step 45: EM did not converge in 20 iterations, RMS force 0.032
> step 46: EM did not converge in 20 iterations, RMS force 0.033
> step 47: EM did not converge in 20 iterations, RMS force 0.032
> step 48: EM did not converge in 20 iterations, RMS force 0.033
> step 49: EM did not converge in 20 iterations, RMS force 0.032
> step 50: EM did not converge in 20 iterations, RMS force 0.032
> step 51: EM did not converge in 20 iterations, RMS force 0.033
> step 52: EM did not converge in 20 iterations, RMS force 0.032
> step 53: EM did not converge in 20 iterations, RMS force 0.033
> step 54: EM did not converge in 20 iterations, RMS force 0.032
> step 55: EM did not converge in 20 iterations, RMS force 0.032
> step 56: EM did not converge in 20 iterations, RMS force 0.032
> step 57: EM did not converge in 20 iterations, RMS force 0.032
> step 58: EM did not converge in 20 iterations, RMS force 0.032
> step 59: EM did not converge in 20 iterations, RMS force 0.032
> step 60: EM did not converge in 20 iterations, RMS force 0.032
> step 61: EM did not converge in 20 iterations, RMS force 0.032
> step 62: EM did not converge in 20 iterations, RMS force 0.032
> step 63: EM did not converge in 20 iterations, RMS force 2.835
> step 64: EM did not converge in 20 iterations, RMS force 120.556
> step 65: EM did not converge in 20 iterations, RMS force 346.147
> step 66: EM did not converge in 20 iterations, RMS force 634.393
> step 67: EM did not converge in 20 iterations, RMS force 904.684
> step 68: EM did not converge in 20 iterations, RMS force 1133.427
> step 69: EM did not converge in 20 iterations, RMS force 735.408
> step 70: EM did not converge in 20 iterations, RMS force 948.153
> step 71: EM did not converge in 20 iterations, RMS force 967.569
> step 72: EM did not converge in 20 iterations, RMS force 630.741
> step 73: EM did not converge in 20 iterations, RMS force 1035.501
> step 74: EM did not converge in 20 iterations, RMS force 698.937
> step 75: EM did not converge in 20 iterations, RMS force 1179.575
> step 76: EM did not converge in 20 iterations, RMS force 765.233
> step 77: EM did not converge in 20 iterations, RMS force 939.995
> step 78: EM did not converge in 20 iterations, RMS force 131.329
> step 79: EM did not converge in 20 iterations, RMS force 51.797
> step 80: EM did not converge in 20 iterations, RMS force 405.775
> step 81: EM did not converge in 20 iterations, RMS force 161.922
> step 82: EM did not converge in 20 iterations, RMS force 565.036
> step 83: EM did not converge in 20 iterations, RMS force 1014.157
> step 84: EM did not converge in 20 iterations, RMS force 1136.628
> step 85: EM did not converge in 20 iterations, RMS force 0.033
> step 86: EM did not converge in 20 iterations, RMS force 307.819
> step 87: EM did not converge in 20 iterations, RMS force 0.032
> step 88: EM did not converge in 20 iterations, RMS force 52.057
> step 89: EM did not converge in 20 iterations, RMS force 0.032
> step 90: EM did not converge in 20 iterations, RMS force 0.032
> step 91: EM did not converge in 20 iterations, RMS force 0.033
> step 92: EM did not converge in 20 iterations, RMS force 251.725
> step 93: EM did not converge in 20 iterations, RMS force 0.032
> step 94: EM did not converge in 20 iterations, RMS force 0.033
> step 95: EM did not converge in 20 iterations, RMS force 0.033
> step 96: EM did not converge in 20 iterations, RMS force 0.033
> step 97: EM did not converge in 20 iterations, RMS force 0.032
> step 98: EM did not converge in 20 iterations, RMS force 0.032
> step 99: EM did not converge in 20 iterations, RMS force 0.032
> step 100: EM did not converge in 20 iterations, RMS force 0.032
> step 101: EM did not converge in 20 iterations, RMS force 0.032
> step 102: EM did not converge in 20 iterations, RMS force 0.032
> step 103: EM did not converge in 20 iterations, RMS force 0.032
> step 104: EM did not converge in 20 iterations, RMS force 0.034
> step 105: EM did not converge in 20 iterations, RMS force 0.033
> step 106: EM did not converge in 20 iterations, RMS force 0.033
> step 107: EM did not converge in 20 iterations, RMS force 0.032
> step 108: EM did not converge in 20 iterations, RMS force 0.032
> step 109: EM did not converge in 20 iterations, RMS force 0.032
> step 110: EM did not converge in 20 iterations, RMS force 0.032
> step 111: EM did not converge in 20 iterations, RMS force 0.032
> step 112: EM did not converge in 20 iterations, RMS force 0.032
> step 113: EM did not converge in 20 iterations, RMS force 0.032
> step 114: EM did not converge in 20 iterations, RMS force 0.032
> step 115: EM did not converge in 20 iterations, RMS force 0.032
> step 116: EM did not converge in 20 iterations, RMS force 0.032
> step 117: EM did not converge in 20 iterations, RMS force 0.032
> step 118: EM did not converge in 20 iterations, RMS force 0.032
> step 119: EM did not converge in 20 iterations, RMS force 0.032
> step 120: EM did not converge in 20 iterations, RMS force 0.032
> step 121: EM did not converge in 20 iterations, RMS force 0.032
> step 122: EM did not converge in 20 iterations, RMS force 0.033
> step 123: EM did not converge in 20 iterations, RMS force 0.033
> step 124: EM did not converge in 20 iterations, RMS force 0.031
> step 125: EM did not converge in 20 iterations, RMS force 0.032
> step 126: EM did not converge in 20 iterations, RMS force 0.033
> step 127: EM did not converge in 20 iterations, RMS force 0.031
> step 128: EM did not converge in 20 iterations, RMS force 0.033
> step 129: EM did not converge in 20 iterations, RMS force 0.031
> step 130: EM did not converge in 20 iterations, RMS force 0.032
> step 131: EM did not converge in 20 iterations, RMS force 0.033
> step 132: EM did not converge in 20 iterations, RMS force 0.032
> step 133: EM did not converge in 20 iterations, RMS force 0.032
> ......
> the swm4-ndp model :
> ;
> ; Topology file for SSWM4-NDP
> ;
> ; Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D.
> ; A polarizable model of water for molecular dynamics simulations of
> biomolecules.
> ; Chem. Phys. Lett. 2006, 418 (1-3), 245-249.
> ;
> ; Possible defines that you can put in your topol.top:
> ; -FLEXIBLE Flexible model
> ; -DPOSRES_WATER Position restrain oxygen atoms
> ;
> [ moleculetype ]
> ; molname nrexcl
> SOL 2
> [ atoms ]
> ; id at type res nr res name at name cg nr charge mass
> 1 OW_swm4ndp 1 SOL OW 1 1.71636 15.99940
> 2 HW_swm4ndp 1 SOL HW1 1 0.55733 1.00800
> 3 HW_swm4ndp 1 SOL HW2 1 0.55733 1.00800
> 4 MW_swm4ndp 1 SOL MW 1 -1.11466 0.00000
> 5 OD_swm4ndp 1 SOL OD 1 -1.71636 0.00000
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 5 1 0.00097825
> #ifndef FLEXIBLE
> [ settles ]
> ; i funct doh dhh
> 1 1 0.09572 0.15139
> #else
> [ bonds ]
> ; i j funct length force.c.
> 1 2 1 0.09572 502416.0
> 1 3 1 0.09572 502416.0
>
> [ angles ]
> ; i j k funct angle force.c.
> 2 1 3 1 104.52 628.02
> #endif
>
> [ dummies3 ]
> ; The position of the dummies is computed as follows:
> ;
> ; O
> ;
> ; D
> ;
> ; H H
> ;
> ; 2 * b = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
> ; 0.024034 nm / [ cos (104.52 / 2 deg) * 0.09572 nm ]
> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-X1)
> ;
> ; Dummy from funct a b
> 4 1 2 3 1 0.205109464 0.205109464
> [ 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
> the ion parameters in conjuction with it:
> ; Topology file for Polarizable Alkali and Halide Ions in conjuction
> with SWM4-NDP water model
> ;
> ; Yu, H. B.; Whitfield, T. W.; Harder, E.; Lamoureux, G.; Vorobyov,
> I.; Anisimov, V. M.; MacKerell, A. D.; Roux, B.
> ; Simulating Monovalent and Divalent Ions in Aqueous Solution Using a
> Drude Polarizable Force Field
> ; J. Chem. Theory Comput. 2010, 6 (3), 774-786.
> [ moleculetype ]
> ; molname nrexcl
> F 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 Fc 1 Fc Fc 1 1.319199
> 2 Fs 1 Fs Fs 1 -2.319199
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 2 1 0.001786
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2
> 2 1
> [ moleculetype ]
> ; molname nrexcl
> CL 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 CLc 1 CLc CLc 1 2.457187
> 2 CLs 1 CLs CLs 1 -3.457187
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 2 1 0.003969
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2
> 2 1
> [ moleculetype ]
> ; molname nrexcl
> BR 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 BRc 1 BRc BRc 1 2.980713
> 2 BRs 1 BRs BRs 1 -3.980713
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 2 1 0.005262
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2
> 2 1
> [ moleculetype ]
> ; molname nrexcl
> I 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 Ic 1 Ic Ic 1 3.733085
> 2 Is 1 Is Is 1 -4.733085
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 2 1 0.007439
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2
> 2 1
> [ moleculetype ]
> ; molname nrexcl
> LI 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 LIc 1 LIc LIc 1 1.310427
> 2 LIs 1 LIs LIs 1 -0.310427
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 2 1 0.000032
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2
> 2 1
> [ moleculetype ]
> ; molname nrexcl
> NA 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 NAc 1 NAc NAc 1 1.687597
> 2 NAs 1 NAs NAs 1 -0.687597
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 2 1 0.000157
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2
> 2 1
> [ moleculetype ]
> ; molname nrexcl
> K 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 Kc 1 Kc Kc 1 2.580968
> 2 Ks 1 Ks Ks 1 -1.580968
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 2 1 0.00083
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2
> 2 1
> [ moleculetype ]
> ; molname nrexcl
> RB 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 RBc 1 RBc RBc 1 3.031161
> 2 RBs 1 RBs RBs 1 -2.031161
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 2 1 0.00137
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2
> 2 1
> [ moleculetype ]
> ; molname nrexcl
> CS 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 CSc 1 CSc CSc 1 3.665877
> 2 CSs 1 CSs CSs 1 -2.665877
> [ polarization ]
> ; See notes above. alpha (nm^3)
> 1 2 1 0.00236
> [ exclusions ]
> ; iatom excluded from interaction with i
> 1 2
> 2 1
> Anybody could give me some helps ?
> Thanks in advance!
> ZHONGJIN HE
>
>
>
--
any problem worth attack
proves its worth by fighting back
Piet Heins "Grooks"
D.G. Sprous, PhD
BioLeap Inc.
Cambridge MA 02141
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