[gmx-users] SWM4-NDP WATER MODEL AND IONS
David van der Spoel
spoel at xray.bmc.uu.se
Fri Feb 10 23:11:05 CET 2012
Op 10 feb 2012 om 22:55 heeft Abhijeet Joshi <abhijoshi129 at gmail.com> het volgende geschreven:
> Hi ,
> I am also working on similar systems. Can you tell me where and what LJ parameters you specified for halides
You need the anharmonic term for polarisation. It is implemented in the development version of 4.6. No manual entry yet. Even with this term F- is difficult to get stable.
> Thanks in advance,
> Abhijeet
>
> On Fri, Aug 12, 2011 at 8:56 AM, zhongjin <zhongjin1000 at yahoo.com.cn> 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
>
> --
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>
>
> --
> Abhijeet Joshi
> Research Assistant
> Molecular Thermodynamics and Statistical Mechanics Research Group
> University of Wisconsin-Madison
> http://www.engr.wisc.edu/groups/mtsm/index.shtml
> aajoshi2 at wisc.edu
> 608-320-9215
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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