Re: Fwd: TIP4P and CHARMM27

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 27 2015 - 10:18:28 CST

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--047d7b5d4c44aa97930525880a1e--

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