Re: Water is boiling with namd and charmm

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Mon Apr 13 2009 - 10:25:43 CDT

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

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