From: uma mageshwari (mageshwariuma6_at_gmail.com)
Date: Wed Jan 28 2009 - 04:11:57 CST
I am running a dynamics for protein-dna complex(nucleosome) in vacuum
2.I think i am in need of PBC eventhough i dont have solvent. Because in a
paper it is given that molecules will evaporate wen there is no boundary
conditions.Is it so?
3.Minimisation is ok.Energy is keep on decreasing. But in the case of
simulation there is sudden increase in the energy and generating numbers
99999999.99999. i dont know why?
I have included my configuration file also. have a look at this.
timestep 0.000000002 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 128. 0. 0.
cellBasisVector2 0. 199. 0.
cellBasisVector3 0. 0. 53.
cellOrigin 56. 100. 8.
# PME (for full-system periodic electrostatics)
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
restartfreq 500 ;# 500steps = every 1ps
run 10000 ;# 5ps
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