From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 06 2015 - 00:59:02 CST
Hi Tristan:
I wrote "a special metal ion". It is really a very special kind of ion,
about which the only chance of using charmm is to be able to translate the
oplsaa vdw and adapt the namd input to that.
cheers
francesco
On Thu, Nov 5, 2015 at 11:19 PM, Tristan Croll <tristan.croll_at_qut.edu.au>
wrote:
> Hi Francesco,
>
>
>
> Before going to that trouble, you might want to look into the latest
> CHARMM forcefield release. Under stream/misc you’ll find
> toppar_ions_won.str, which has a pretty comprehensive list of metal ions.
> I’ve pasted the header below.
>
>
>
> Cheers,
>
>
>
> Tristan
>
>
>
> * top_ions_won.str: general model for mono-, di-, and trivalent cations
>
> *
>
>
>
> !This is a comprehensive set of ions developed using stochastic boundary
>
> !conditions. It is strongly recommended that ion parameters in
>
> !toppar_water_ions.str be used if available, as they are more highly
>
> !optimized. Accordingly, those ions have been commented in this
>
> !file.
>
> !
>
> !reference
>
> !Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations
>
> !Developed under the Solvent Boundary Potential," Journal of Physical
>
> !Chemistry A., 116: 11763-11767, 2012.
>
>
>
>
>
> !test "append" to determine if previous toppar files have been read and
>
> !add append to "read rtf card" if true
>
> set nat ?NATC
>
> set app
>
> !We're exploiting what is arguably a bug in the parser. On the left hand
> side,
>
> !the quotes have priority, so NAT is correctly substituted. On the right
> hand
>
> !side, the ? has priority and NATC" (sic) is not a valid substitution...
>
> if "@NAT" ne "?NATC" if @nat ne 0 set app append
>
>
>
> read rtf card @app
>
> * Topology for water and ions
>
> *
>
> 37 1
>
>
>
> ! J. Phys. Chem. B Supporting Information, October 12, 2012
>
> !Mass 301 Li1p 6.940 Li ! Lithium
>
> !Mass 302 Na1p 22.990 Na ! Sodium
>
> !Mass 303 K1p 39.098 K ! Potassium
>
> !Mass 304 Rb1p 85.468 Rb ! Rubidium
>
> !Mass 305 Cs1p 132.91 Cs ! Cesium
>
> Mass 306 Cu1p 63.546 Cu ! Copper
>
> Mass 307 Ag1p 107.87 Ag ! Silver
>
> Mass 308 Au1p 196.97 Au ! Gold
>
> Mass 309 Ti1p 47.867 Ti ! Titanium
>
> Mass 321 Be2p 9.0122 Be ! Beryllium
>
> !Mass 322 Mg2p 24.305 Mg ! Magnesium
>
> !Mass 323 Ca2p 40.078 Ca ! Calcium
>
> Mass 324 Sr2p 87.62 Sr ! Strontium
>
> !Mass 325 Ba2p 137.33 Ba ! Barium
>
> Mass 326 Ra2p 226.03 Ra ! Radium
>
> Mass 327 V2p 50.942 V ! Vanadium
>
> Mass 328 Cr2p 51.996 Cr ! Chromium
>
> Mass 329 Mn2p 54.938 Mn ! Manganese
>
> Mass 330 Fe2p 55.854 Fe ! Iron
>
> Mass 331 Co2p 58.933 Co ! Cobalt
>
> Mass 332 Ni2p 58.693 Ni ! Nickel
>
> Mass 333 Cu2p 63.546 Cu ! Copper
>
> !Mass 334 Zn2p 65.38 Zn ! Zinc
>
> Mass 335 Pd2p 106.42 Pd ! Palladium
>
> Mass 336 Ag2p 107.87 Ag ! Silver
>
> !Mass 337 Cd2p 112.41 Cd ! Cadmium
>
> Mass 338 Sn2p 118.71 Sn ! Tin
>
> Mass 339 Pt2p 195.08 Pt ! Platinum
>
> Mass 340 Hg2p 200.59 Hg ! Mercury
>
> Mass 341 Pb2p 207.20 Pb ! Lead
>
> Mass 342 Sm2p 150.36 Sm ! Samarium
>
> Mass 343 Eu2p 151.96 Eu ! Europium
>
> Mass 344 Yb2p 173.05 Yb ! Ytterbium
>
> Mass 351 Al3p 26.982 Al ! Aluminum
>
> Mass 352 Sc3p 44.956 Sc ! Scandium
>
> Mass 353 Y3p 88.906 Y ! Yttrium
>
> Mass 354 La3p 138.91 La ! Lanthanum
>
> Mass 355 Ce3p 140.12 Ce ! Cerium
>
> Mass 356 Pr3p 140.91 Pr ! Praseodynium
>
> Mass 357 Nd3p 144.24 Nd ! Neodynium
>
> Mass 358 Pm3p 144.91 Pm ! Promethium
>
> Mass 359 Sm3p 150.36 Sm ! Samarium
>
> Mass 360 Eu3p 151.96 Eu ! Europium
>
> Mass 361 Gd3p 157.25 Gd ! Gadolinium
>
> Mass 362 Tb3p 158.93 Tb ! Terbium
>
> Mass 363 Dy3p 162.50 Dy ! Dysprosium
>
> Mass 364 Ho3p 164.93 Ho ! Holmium
>
> Mass 365 Er3p 167.28 Er ! Erbium
>
> Mass 366 Tm3p 168.93 Tm ! Thulium
>
> Mass 367 Yb3p 173.05 Yb ! Ytterbium
>
> Mass 368 Lu3p 174.97 Lu ! Lutetium
>
> Mass 369 U3p 238.03 U ! Uranium
>
> Mass 370 Pu3p 244.06 Pu ! Plutonium
>
> Mass 371 Ti3p 47.867 Ti ! Titanium
>
> Mass 372 V3p 50.942 V ! Vanadium
>
> Mass 373 Cr3p 51.996 Cr ! Chromium
>
> Mass 374 Mn3p 54.938 Mn ! Manganese
>
> Mass 375 Fe3p 55.854 Fe ! Iron
>
> Mass 376 Co3p 58.933 Co ! Cobalt
>
> Mass 377 Ga3p 69.723 Ga ! Gallium
>
> Mass 378 Rh3p 102.91 Rh ! Rhodium
>
> Mass 379 In3p 114.82 In ! Indium
>
> Mass 380 Au3p 196.97 Au ! Gold
>
> Mass 381 Tl3p 204.38 Tl ! Thallium
>
> Mass 382 Bi3p 208.98 Bi ! Bismuth
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Francesco Pietra
> *Sent:* Friday, 6 November 2015 2:22 AM
> *To:* NAMD
> *Subject:* namd-l: OPLSAA to CHARMM
>
>
>
> Hello:
>
> I am getting troubles in converting (for a special ion) good oplsaa vdw
> params to charmm. That is, rdf shows the expected octahedral solvation by
> TIP3P water on MD for the ion in water, however the metal-O distances are
> by some 20% too large (namd2.10 under following settings:
>
> # temperature control
> # temperature 300
> langevin on
> langevinTemp 300
> langevinDamping 5
> langevinHydrogen off
>
> # constant pressure control
> useGroupPressure yes
> useFlexibleCell no
> UseConstantArea no
> useConstantRatio no
> LangevinPiston on
> LangevinPistonTarget 1.01325
> LangevinPistonPeriod 200
> LangevinPistonDecay 100
> LangevinPistonTemp 300
>
> # integrator
> timestep 1.5 # 1.5 fs/step
> nonbondedFreq 1 # nonbonded forces every step
> fullElectFrequency 5 # PME only every five step
> stepspercycle 20 # redo pairlist every 20 steps
>
> # Approximations
> # rigidBonds all ;# needed for 2fs/step
> rigidBonds water
> rigidTolerance 0.000001
> exclude scaled1-4
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 13.5 # cutoff +3.5
> margin 0
> 1-4scaling 1.0
> PME yes
>
>
> By adding
>
> vdwGeometricSigma yes
>
> minimization of the system does not go on (halting at the tcl request:
> .................
> Info: CREATING 68 COMPUTE OBJECTS
> Info: useSync: 1 useProxySync: 0
> Info: Startup phase 10 took 0.000324965 s, 118.027 MB of memory in use
> Info: Startup phase 11 took 3.60012e-05 s, 118.027 MB of memory in use
> Info: Startup phase 12 took 3.69549e-05 s, 118.156 MB of memory in use
> Info: Finished startup at 0.0427089 s, 118.156 MB of memory in use
>
> TCL: Running for 1000 steps
>
> which is not surprising because there are also normal charmm params for
> TIP3P water.
>
> Thanks for advice about oplsaa -> charmm params conversion
>
> francesco pietra
>
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