From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Mon Apr 13 2009 - 11:42:38 CDT
Hi,
adjusting the dimensions of your box probably won't solve the problem.
You should:
(1) run at constant pressure while you heat up your system.
(2) start a short, additional run at constant pressure at T=300K
in order to "equilibrate" your box dimension (check your xst file)
After your box is "equilibrated" you can start your run at constant
volume under NVT conditions.
-g
> 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
>
>
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