From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 27 2015 - 11:35:25 CST
Hi Peter:
I had taken the MD conf, adapted to min, with the mistake that you picked
out.
The system could now be brought to 300K easily, now. Equilibration will
tell whether, with my CHARMM27 adaptation, the solvation of the model ion
in the simulation is what is experimentally known for the real ion.
Thanks, thanks
francesco
On Fri, Nov 27, 2015 at 5:26 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:
> Hi Francesco,
> This config file doesn’t actually minimize the system, though.
> “minimization on” says that conjugate gradient minimization should be used,
> but unless you actually say
> minimize 1000
>
> it will try to run dynamics when you give the run command. This is
> probably why the system is blowing up; it isn’t actually being minimized
> prior to running.
>
> Best,
> Peter
>
> > On Nov 27, 2015, at 11:18 AM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
> >
> > Hi Peter:
> >
> >
> > Are you using a system with all OPLSAA parameters, or mixing an OPLSAA
> molecule with other molecules that have charmm parameters (eg, charmm27
> protein)?
> >
> > No, the OPLSAAA parameters were translated for CHARMM27. With other
> TIP3P-solvated models that worked nicely. Also, I carried out test
> "trasnlations" for various atoms.
> >
> > Could you post your config file?
> >
> > You have it below, it was the initial (not crashing) minimization. It
> was used either with the listed constraints or without any constraint. I
> was trying to carry out a RDF checking the quality of the TIP4P solvation
> of the ion, stability, geometry, distances. I am familiar with that for
> TIP3P solvation in other cases.
> >
> > # forcefield
> > paratypecharmm on
> > parameters ./tip4p.par # provided by Freddolino
> > parameters ./myion.prm
> > parameters ./CLA.par # chloride used for neutralizing the system
> because of myion cation
> > waterModel tip4 # according to Freddolino tip4p
> >
> >
> > # molecules
> > structure ./myion_TIP4Pbox_ion.psf
> > coordinates ./myion_TIP4Pbox_ion.pdb
> > # bincoordinates ./min-01.restart.coor
> > # binvelocities ./min-01.restart.vel
> > # extendedSystem ./min-01.restart.xsc
> >
> > ##########################################
> >
> > # constraints
> >
> >
> > if {0} {
> > constraints on
> > consref file
> > conskfile file
> > conskcol B
> > }
> >
> > if {0} {
> > fixedAtoms on
> > fixedAtomsFile file
> > fixedAtomsCol O
> > }
> >
> > ##########################################
> >
> > temperature 0
> >
> > # integrator
> > timestep 0.01 # 0.01 fs/step
> > nonbondedFreq 1 # nonbonded forces every step
> > fullElectFrequency 1 # at each step according to Freddolino tip4p
> > 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 5
> > 1-4scaling 1.0
> > PME yes
> > # Don't set the periodic cell basis if you have also specified an .xsc
> > # restart file
> > cellBasisVector1 21.10 0. 0.
> > cellBasisVector2 0. 21.22 0.
> > cellBasisVector3 0. 0. 21.12
> >
> > cellOrigin -4.011866569519043 29.038618087768555 -20.158430099487305
> >
> > PMEGridSpacing 1.0
> > PMEGridSizeX 31
> > PMEGridSizeY 31
> > PMEGridSizeZ 31
> >
> >
> > # output
> > outputName ./min-01
> > outputEnergies 500 # multiple of fullElectFrequency or viceversa
> > restartfreq 100
> > binaryrestart yes
> > binaryoutput no
> > wrapNearest no
> > wrapAll on
> >
> >
> > # Minimize protocol (steps multiple of stepspercycle)
> >
> > minimization on # default off
> > minTinyStep 1.0e-6 # default 1.0e-6
> > minBabyStep 1.0e-2 # default 1.0e-2
> > minLineGoal 1.0e-4 # default 1.0e-4
> >
> > # velocityQuenching on # default off
> > maximumMove 0.00000001 # default 0.75 x cutoff/stepsPerCycle = 0.5
> >
> > run 1000
> >
> > **************
> >
> > thanks
> >
> > francesco
> >
> >
> > On Fri, Nov 27, 2015 at 4:41 PM, Peter Freddolino <petefred_at_umich.edu>
> wrote:
> > Hi Francesco,
> > Could you post your config file? I’m guessing the water model or
> rigidbonds types are not getting recognized properly.
> > The warning I gave about using TIP4 with charmm force fields does not
> refer to the kind of error that will make your system explode, but just to
> the kind that will make your results questionable (arguably this is worse).
> > I’m confused by the description at the end of the system you’re trying
> to simulate. Are you using a system with all OPLSAA parameters, or mixing
> an OPLSAA molecule with other molecules that have charmm parameters (eg,
> charmm27 protein)? The latter should not be done.
> > Best,
> > Peter
> >
> > > On Nov 27, 2015, at 10:17 AM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
> > >
> > > Hello: Updating previous mail to VMD only. On restarting that work
> from scratch, with my molecule solvated by TIP4P (Freddolino box), I was
> unable to minimize the system, by any protocol of NAMD 2.10, beyond
> ts=0.055fs. Both these and previous minimization at ts=1.2fs (this could
> not be reproduced) did not allow heating NVT: crash at the first step from
> 0 to 1K, because of atoms moving too fast. All those procedure are
> familiar and successful in my quarters with TIP3P. Then, I came across
> warnings that unfortunately I had missed before:
> > >
> > > Things get DICEY very fast if you try using ANY TIP4 models with
> charmm forcefields, because of how deeply the water model is baked into the
> charmm parameterization procedure. People do it, sometimes it seems to work
> well, but there's no reason to expect that it actually SHOULD give
> reasonable results. (Freddolino 29-Sep-2015, at 7:25 PM)
> > >
> > > All my efforts above were prompted by having got a TIP4P-solvated atom
> model that had been parameterized with OPLSAA in GROMACS (while I know how
> to change those type of parameters to charmm27). I wonder now whether that
> model was reliable work.
> > >
> > > cheers
> > >
> > > francesco pietra
> > >
> > > ---------- Forwarded message ----------
> > > From: Francesco Pietra <chiendarret_at_gmail.com>
> > > Date: Thu, Nov 26, 2015 at 10:50 PM
> > > Subject: TIP4P and CHARMM27
> > > To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
> > >
> > >
> > > Hello:
> > > For practical reasons I would like to use TIP4P water (Freddolino kit)
> with CHARMM27, not 36 ff (I have params for ligands ready in the 27 ff).
> > >
> > > Water is also a ligand at the active site (starting PDB file), and
> that also should be TIP4P. Is that conceivable? Also, should TIP4P in the
> solvated system be constrained as indicated in the example provided by Prof
> Freddolino during minimization, NVT heating, NPT? In the final productive
> NPT I would like not to constrain any bond in the protein.
> > >
> > > In preliminary trials without constraining anything, minimization run
> plainly up to ts=1.0fs; atoms moving too fast beyond that.
> > >
> > > Thanks for advice
> > >
> > > francesco pietra
> > >
> >
> >
>
>
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