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

zhongjin zhongjin1000 at yahoo.com.cn
Fri Aug 12 15:56:29 CEST 2011


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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