From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 27 2015 - 15:54:56 CST

Hi Peter:
Recomputed according to the different units. Negligible difference for bond
and angle forces, distances from nm to A. neither dihedrals (<kT with my
metals) nor impropers needed in my case, otherwise it would not be easy
given the difference of treatment with GROMACS and CHARMM.

Big difference with nonbonded. Epsilon = GROMCS/4.18 (scaled 0.5 x
epsilon). Sigma comes from (GROMACSx10) x 1/2 x 2^-6.

cheers
francesco

On Fri, Nov 27, 2015 at 6:37 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> Hi Francesco,
> I’m glad this worked. I admit I’m still confused on this “CHARMM27
> adaptation” business. Are you simply reformatting OPLS parameters to the
> charmm parameter format, or is there something deeper going on?
> Best,
> Peter
>
> > On Nov 27, 2015, at 12:35 PM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
> >
> > 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
> > > >
> > >
> > >
> >
> >
>
>