[gmx-users] Re: [gmx-developers] shell polarizable water model
Jochen Hub
jhub at gwdg.de
Fri Oct 12 18:00:36 CEST 2012
Hi,
please google for "polarization catastrophe". There is is a good review
by Van Gunsteren on this issue. I am afraid there is not a simple
solution for your problem. You may want to try the swm4-dp model, which
was more stable in our simulations.
Cheers,
Jochen
Am 10/11/12 8:36 PM, schrieb Ananya Mondal:
> Hi Mikhail,
> I am using GMX4.5.5 to simulate SWM4-NDP polarizable water model, it
> is working fine.
> When i am running separately NA+ polarizable ion in SWM4-NDP water
> and Cl- polarizable ion in SWM4-NDP polarizable water model, it is
> working fine.
> But when I use the both NA+ and CL- (NaCl salt solution) polarizable
> model which is in conjuction with SWM4-NDP model, the RMS force is
> very large:
>
> can anyone give some idea, what i am missing..
> Thanking you
> Ananya
>
> here is my itp file
> [ defaults ]
> LJ Geometric
> [ atomtypes ]
> ;name mass charge ptype c6 c12
> WO 15.99940 0.0 A 0.0 0.0
> WH 1.00800 0.0 A 0.0 0.0
> WS 0.0 0.0 S 0.0 0.0
> WD 0.0 0.0 D 0.0 0.0
> NAc 22.989769 0.0 A 0.0 0.0
> NAs 0.0000000 0.0 S 0.0 0.0
> CLc 35.45300 0.0 A 0.0 0.0
> CLs 0.0000000 0.0 S 0.0 0.0
> [ nonbond_params ]
> WO WO 1 3.67796770E-03 3.83182123E-06
> WO NAc 1 7.84740725E-04 4.51332937E-07
> WO CLc 1 6.24036649E-03 1.83075990E-05
> NAc NAc 1 1.56840324E-04 4.66461074E-08
> CLc CLc 1 9.08923242E-03 6.44595639E-05
> NAc CLc 1 1.46880350E-03 2.62418143E-06
> [ moleculetype ]
> ; molname nrexcl
> SM2 2
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 WO 1 SM2 OW1 1 1.71636
> 2 WH 1 SM2 HW2 1 0.55733
> 3 WH 1 SM2 HW3 1 0.55733
> 4 WD 1 SM2 DW 1 -1.11466
> 5 WS 1 SM2 SW 1 -1.71636
> [ polarization ]
> 1 5 1 0.00097822
> [ constraints ]
> ; i funct doh dhh
> 1 2 1 0.09572
> 1 3 1 0.09572
> 3 2 1 0.15139
> [ virtual_sites3 ]
> 4 1 2 3 2 0.5 0.024034
> [ 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
> [ 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
> Cl- 1
>
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 CLc 1 ion CLc 1 2.457187
> 2 CLs 1 ion 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
>
> here is my g.mdb file
>
> include =
> define =
> integrator = md
> tinit = 0
> dt = 0.0005
> nsteps = 1000000
> init_step = 0
> simulation_part = 1
> comm-mode = Linear
> nstcomm = 10
> comm-grps = system
> bd-fric = 0
> ld-seed = 1993
> emtol = 0.1
> emstep = 0.01
> niter = 30
> fcstep = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> rtpi = 0.05
> nstxout = 10
> nstvout = 00
> nstfout = 0
> nstlog = 50
> nstcalcenergy = -1
> nstenergy = 10
> nstxtcout = 250
> xtc-precision = 1000
> xtc-grps =
> energygrps = System
> nstlist = 5
> ns-type = grid
> pbc = xyz
> rlist = 0.75
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 0.75
> epsilon_r = 1
> epsilon_rf = 1
> vdw-type = Cut-off
> rvdw-switch = 0
> rvdw = 0.75
> DispCorr = EnerPres
> table-extension = 1
> energygrp_table =
> fourierspacing = 0.12
> fourier_nx = 32
> fourier_ny = 32
> fourier_nz = 32
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
> gb_algorithm = Still
> nstgbradii = 0
> rgbradii = 0
> gb_saltconc = 0
> implicit_solvent = No
> tcoupl = nose-hoover
> nsttcouple = -1
> nh-chain-length = 10
> tc-grps = system
> tau-t = 0.05
> ref-t = 300
> gen-vel = yes
> gen-temp = 300
> gen-seed = 173529
> constraints = all-bonds
> constraint-algorithm = shake
> continuation = no
> Shake-SOR = no
> shake-tol = 0.0001
> lincs-order = 4
> lincs-iter = 2
> lincs-warnangle = 30
> morse = no
> energygrp_excl =
> nwall = 0
> wall_type = 9-3
> wall_r_linpot = -1
> wall_atomtype =
> wall_density =
> wall_ewald_zfac = 3
> pull = no
> disre = No
> disre-weighting = Conservative
> disre-mixed = no
> disre-fc = 1000
> disre-tau = 0
> nstdisreout = 100
> orire = no
> orire-fc = 0
> orire-tau = 0
> orire-fitgrp =
> nstorireout = 100
> dihre = no
> dihre-fc = 1000
> free-energy = no
> init-lambda = 0
> delta-lambda = 0
> foreign_lambda =
> sc-alpha = 0
> sc-power = 0
> sc-sigma = 0.3
> nstdhdl = 10
> separate-dhdl-file = yes
> dhdl-derivatives = yes
> dh_hist_size = 0
> dh_hist_spacing = 0.1
> couple-moltype =
> couple-lambda0 = vdw-q
> couple-lambda1 = vdw-q
> couple-intramol = no
> userreal4 = 0
>
--
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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