[gmx-users] SWM4-NDP WATER MODEL AND IONS

Abhijeet Joshi abhijoshi129 at gmail.com
Fri Feb 10 22:55:18 CET 2012


Hi ,
        I am also working on similar systems. Can you tell me where and
what LJ parameters you specified for halides

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
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