expansion of solvation box at high temperature

From: mjyang (mjyang_at_hku.hk)
Date: Sun Oct 17 2010 - 02:03:31 CDT

Dear NAMD users,

   I performed a simulation of a protein + TIP3 water system at 600K. But after 2 ns production run under NPT ensemble, the volume of solvation box expanded by more than 1000 times and the mass density reduced from 1.05909 g/cm^3 to 0.000607189 g/cm^3. I am not sure whether this phenomenan is caused by NPT ensemble at hight temperature or any other factors.

The following three NPT schemes were tested and the expansion occured in all cases:
scheme a: temperature control 1 and pressure control 1
scheme b: temperature control 1 and pressure control 2
scheme c: temperature control 2 and pressure control 2

Could someone please tell me how to fix this problem?

------------------------
Temperature control:
1.
     langevin on ;# do langevin dynamics
    langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
    langevinTemp $temperature
    langevinHydrogen no ;# don't couple langevin bath to hydrogens

2.
    tcouple on
    tcoupletemp $temperature

Pressure control:
1.
   useGroupPressure yes ;# needed for 2fs steps
    useFlexibleCell no ;# no for water box, yes for membrane
    useConstantArea no ;# no for water box, yes for membrane

    berendsenpressure on
    berendsenpressuretarget 1.01325
    berendsenpressurecompressibility 4.57e-5
    berendsenpressurerelaxationtime 100
    berendsenpressurefreq 10

2.
    useGroupPressure yes ;# needed for 2fs steps
    useFlexibleCell no ;# no for water box, yes for membrane
    useConstantArea no ;# no for water box, yes for membrane

    langevinPiston on
    langevinPistonTarget 1.01325 ;# in bar -> 1 atm
    langevinPistonPeriod 100.
    langevinPistonDecay 50.
    langevinPistonTemp $temperature
    SurfaceTensionTarget 0.0 ;
-----------------------------

Thanks for the time.

Mingjun

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