[gmx-users] SWM4-NDP WATER MODEL AND IONS
Abhijeet Joshi
abhijoshi129 at gmail.com
Fri Feb 10 23:19:08 CET 2012
On Fri, Feb 10, 2012 at 4:11 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:
>
> Op 10 feb 2012 om 22:55 heeft Abhijeet Joshi <abhijoshi129 at gmail.com> 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 <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
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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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
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at
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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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