From: ahenneck_at_ix.urz.uni-heidelberg.de
Date: Tue Mar 06 2007 - 04:27:03 CST
Dear NAMD users
I observe a total energy increase of about 70kcal/ns in my NVE
dynamics simulations (TOTAL, TOTAL2 and TOTAL3 are increasing,
potential and kinetic energy are stable).
This does not occur with a timestep of 1 fs, however since I fix all
bonds to hydrogen atoms, a 2fs timestep should work as well.
If anybody has run stable NVE simulations using the CHARMM22 force
field, I'd be happy to get the simulation parameters optimized to this
force field or a suggestion on how to better conserve the total energy.
Cheers
Anna
My setup:
- short (11 residue) aspartic-acid-rich peptide in explicit water
(periodic boundary conditions)
- The system was heated slowly. Equilibration was done in three steps,
gradually releasing constraints from the peptide and using velocity
rescaling every 500 timesteps
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters /home/par_all22_prot.inp
# temperature 300
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 10.
switching on
switchdist 9.
pairlistdist 11.5
# Integrator Parameters
timestep 2.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin off
#langevinDamping 1
#langevinTemp 300
#langevinHydrogen off
# Periodic Boundary Conditions
cellBasisVector1 70. 0. 0.
cellBasisVector2 0. 70. 0.
cellBasisVector3 0. 0 70.
cellOrigin 0. 0. 0.
# Image center all molecules
wrapAll on
wrapNearest on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 61
PMEGridSizeY 61
PMEGridSizeZ 61
# Order default 4 (cubic):
PMEInterpOrder 6
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