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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