[gmx-users] RMS force is very large for shell MD
zhongjin
zhongjin1000 at yahoo.com.cn
Mon Aug 15 11:13:04 CEST 2011
Dear gmx users:
I have read a paper"Atomistic simulation of ion solvation in water explains surface preference of halides", I think it is a perfect work. And I am also interested in the electrolyte behavior at interface. I am using SWM4-NDP polarizable water model and ion Polarizable Alkali and Halide Ions in conjuction with SWM4-NDP water model by GMX4.5.4, I find the RMS force is very large, and at last the system blow up. BUT I simulate pure water with SWM4-NDP water model , It seems everything is OK.I need your help, thanks in advance.
Best wishes!
Zhongjin He
The error:
step 177: EM did not converge in 20 iterations, RMS force 0.032
step 178: EM did not converge in 20 iterations, RMS force 0.033
step 179: EM did not converge in 20 iterations, RMS force 0.033
step 180: EM did not converge in 20 iterations, RMS force 0.033
step 181: EM did not converge in 20 iterations, RMS force 0.032
step 182: EM did not converge in 20 iterations, RMS force 0.033
step 183: EM did not converge in 20 iterations, RMS force 0.033
step 184: EM did not converge in 20 iterations, RMS force 0.033
step 185: EM did not converge in 20 iterations, RMS force 0.032
step 186: EM did not converge in 20 iterations, RMS force 0.033
step 187: EM did not converge in 20 iterations, RMS force 0.032
step 188: EM did not converge in 20 iterations, RMS force 0.033
step 189: EM did not converge in 20 iterations, RMS force 0.033
step 190: EM did not converge in 20 iterations, RMS force 0.032
step 191: EM did not converge in 20 iterations, RMS force 0.033
step 192: EM did not converge in 20 iterations, RMS force 0.033
step 193: EM did not converge in 20 iterations, RMS force 0.033
step 194: EM did not converge in 20 iterations, RMS force 0.035
step 195: EM did not converge in 20 iterations, RMS force 0.042
step 196: EM did not converge in 20 iterations, RMS force 1.898
step 197: EM did not converge in 20 iterations, RMS force 49.403
step 198: EM did not converge in 20 iterations, RMS force 173.436
step 199: EM did not converge in 20 iterations, RMS force 363.106
step 200: EM did not converge in 20 iterations, RMS force 589.073
step 201: EM did not converge in 20 iterations, RMS force 786.105
step 202: EM did not converge in 20 iterations, RMS force 845.617
step 203: EM did not converge in 20 iterations, RMS force 773.659
step 204: EM did not converge in 20 iterations, RMS force 741.854
step 205: EM did not converge in 20 iterations, RMS force 778.916
step 206: EM did not converge in 20 iterations, RMS force 964.226
step 207: EM did not converge in 20 iterations, RMS force 1340.912
step 208: EM did not converge in 20 iterations, RMS force 1790.702
step 209: EM did not converge in 20 iterations, RMS force 488.729
step 210: EM did not converge in 20 iterations, RMS force 820.419
step 211: EM did not converge in 20 iterations, RMS force 977.581
step 212: EM did not converge in 20 iterations, RMS force 923.088
step 213: EM did not converge in 20 iterations, RMS force 729.115
step 214: EM did not converge in 20 iterations, RMS force 791.220
step 215: EM did not converge in 20 iterations, RMS force 619.807
step 216: EM did not converge in 20 iterations, RMS force 693.143
step 217: EM did not converge in 20 iterations, RMS force 730.895
step 218: EM did not converge in 20 iterations, RMS force 588.245
step 219: EM did not converge in 20 iterations, RMS force 1110.880
step 220: EM did not converge in 20 iterations, RMS force 1146.601
step 221: EM did not converge in 20 iterations, RMS force 509.965
step 222: EM did not converge in 20 iterations, RMS force 198.761
step 223: EM did not converge in 20 iterations, RMS force 78.372
step 224: EM did not converge in 20 iterations, RMS force 472.341
step 225: EM did not converge in 20 iterations, RMS force 873.614
step 226: EM did not converge in 20 iterations, RMS force 1676.297
step 227: EM did not converge in 20 iterations, RMS force 1731.009
step 227: Water molecule starting at atom 2641 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
step 228: EM did not converge in 20 iterations, RMS force 0.040
step 228: Water molecule starting at atom 2641 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
step 229: EM did not converge in 20 iterations, RMS force 0.038
step 230: EM did not converge in 20 iterations, RMS force 0.032
step 230: Water molecule starting at atom 2641 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
step 231: EM did not converge in 20 iterations, RMS force 0.033
step 232: EM did not converge in 20 iterations, RMS force 0.032
step 232: Water molecule starting at atom 2641 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
step 233: EM did not converge in 20 iterations, RMS force 0.032
step 234: EM did not converge in 20 iterations, RMS force 0.032
step 235: EM did not converge in 20 iterations, RMS force 0.032
step 236: EM did not converge in 20 iterations, RMS force 695.555
step 324: EM did not converge in 20 iterations, RMS force 2254.332
step 325: EM did not converge in 20 iterations, RMS force 1366.153
step 325: Water molecule starting at atom 2641 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
step 326: EM did not converge in 20 iterations, RMS force 4453.299
step 326: Water molecule starting at atom 2641 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun, VERSION 4.5.4
Source code file: pme.c, line: 538
Fatal error:
2 particles communicated to PME node 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
ion parameters:
; 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 F Fc 1 1.319199
2 Fs 1 F 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 CL CLc 1 2.457187
2 CLs 1 CL 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 BR BRc 1 2.980713
2 BRs 1 BR 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 I Ic 1 3.733085
2 Is 1 I 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 LI LIc 1 1.310427
2 LIs 1 LI 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 NA NAc 1 1.687597
2 NAs 1 NA 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 K Kc 1 2.580968
2 Ks 1 K 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 RB RBc 1 3.031161
2 RBs 1 RB 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 CS CSc 1 3.665877
2 CSs 1 CS 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
SWM4-NDP water 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
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