Re: Water is boiling with namd and charmm

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Mon Apr 13 2009 - 10:50:31 CDT

How are you setting the cellBasisVector and cellOrigin parameters?
I've generally seen bubbles when the cellBasisVectors were either too
large or too small relative to the actual dimensions of the system,
but then again I usually use a barostat in my simulations. That said,
the amount you rounded shouldn't be a big deal. Also are you using
vmd's "measure center $sel" to get your cellOrigin? Although I've had
this deviate slightly from {0 0 0}, I've never had a system where it
is so askew. I'm not 100% sure if that would cause a problem, but it
looked potentially funny to me.

Josh

On Apr 13, 2009, at 8:25 AM, Roman Petrenko wrote:

> this "boiling" is most likely due to larger water box than the number
> of water molecules.
>
> try to decrease your water box size
> cellBasisVector1 109 0. 0.
> cellBasisVector2 0. 103 0.
> cellBasisVector3 0. 0 106.
>
> say, by 2 A (or by 1A)
> cellBasisVector1 107 0. 0.
> cellBasisVector2 0. 101 0.
> cellBasisVector3 0. 0 104.
>
> there is no need to modify input files, simply make these changes in
> the configuration namd file.
>
> P.S. is your pressure negative?
>
>
> On Mon, Apr 13, 2009 at 10:27 AM, DimitryASuplatov
> <genesup_at_gmail.com> wrote:
>> Hello,
>>
>> I am running 10ns molecular dynamics simulation starting from 0K,
>> then
>> heating to 300K, then followed by 10 ns of free dynamics at 300K.
>> At some point I noticed water "boiling" in the cell - huge bubbles
>> appeared in the water. I guess this happened since I did not set the
>> constant pressure so my system remained at constant volume.
>> Am I correct?
>> I have rounded the cellBasisVector coordinates (lets say, from
>> 108,7 to
>> 109). Could this be the cause?
>> Should I use constant pressure at next simmulation? Configuration
>> file
>> is below.
>>
>> Thanks for your time.
>> SDA
>>
>> #############################################################
>> ## JOB DESCRIPTION ##
>> #############################################################
>>
>> # STRMB in a Water Box
>>
>>
>> #############################################################
>> ## ADJUSTABLE PARAMETERS ##
>> #############################################################
>>
>> structure ./strmb.s.charmm.psf
>> coordinates ./strmb.s.charmm.pdb
>>
>> set start_temperature 0
>> set hold_temperature 300
>> set outputname strmb.md.charmm.namd
>>
>> firsttimestep 0
>>
>>
>> #############################################################
>> ## SIMULATION PARAMETERS ##
>> #############################################################
>>
>> # Input
>> paraTypeCharmm on
>> parameters ./par_all27_prot_lipid.inp
>> temperature $start_temperature
>>
>>
>> # Force-Field Parameters
>> exclude scaled1-4
>> 1-4scaling 1.0
>> cutoff 15.
>> switching on
>> switchdist 10.
>>
>>
>> # Integrator Parameters
>> timestep 2.0 ;# 2fs/step
>> rigidBonds all ;# needed for 2fs steps
>> nonbondedFreq 1
>> fullElectFrequency 2
>> stepspercycle 10
>>
>>
>> # Constant Temperature Control
>> langevin on ;# do langevin dynamics
>> langevinTemp 0
>> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
>> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>>
>>
>> # Periodic Boundary Conditions
>> cellBasisVector1 109 0. 0.
>> cellBasisVector2 0. 103 0.
>> cellBasisVector3 0. 0 106.
>> cellOrigin 63.87940979 13.3578186035 32.2524185181
>>
>> wrapAll on
>>
>>
>> #PME (for full-system periodic electrostatics)
>> PME yes
>> PMEGridSizeX 125
>> PMEGridSizeY 125
>> PMEGridSizeZ 125
>>
>>
>> # Output
>> outputName $outputname
>>
>> restartfreq 10000
>> dcdfreq 2000
>> xstFreq 2000
>> outputEnergies 2000
>> outputPressure 10000
>>
>>
>> #############################################################
>> ## EXTRA PARAMETERS ##
>> #############################################################
>>
>>
>> #############################################################
>> ## EXECUTION SCRIPT ##
>> #############################################################
>>
>>
>> # Minimization
>> minimize 5000
>>
>> #Heat
>> for { set TEMP $start_temperature } { $TEMP < $hold_temperature }
>> { incr
>> TEMP 25 } {
>> langevinTemp $TEMP
>> reassignTemp $TEMP
>> run 5000
>> }
>>
>>
>> reassignTemp $hold_temperature
>> langevinTemp $hold_temperature
>> run 5000000
>>
>>
>>
>>
>>
>>
>>
>
>
>
> --
> Roman Petrenko
> Physics Department
> University of Cincinnati
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
------------------------------------------------------------------------------------------------------

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