Op 10 feb 2012 om 22:55 heeft Abhijeet Joshi <[email protected]> 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 <[email protected]> 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > Abhijeet Joshi > Research Assistant > Molecular Thermodynamics and Statistical Mechanics Research Group > University of Wisconsin-Madison > http://www.engr.wisc.edu/groups/mtsm/index.shtml > [email protected] > 608-320-9215 > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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