On Fri, Feb 10, 2012 at 4:11 PM, David van der Spoel <[email protected]>wrote:
> > 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 a lot David, Could you direct me to some article or reading material regarding this anharmonic term? > 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 > > > -- > 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
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