Protein Deformity in Implicit Solvent Simulation

From: Athena Xue (athenax_at_uchicago.edu)
Date: Sun Sep 01 2019 - 18:46:48 CDT

Hello,

I ran a generalized born implicit solvent simulation on an enzyme-substrate
complex (insulin degrading enzyme and insulin) at 300K, using the default
simulation parameters from the NAMD tutorial. However, the enzyme deformed
during my simulation. I have copied part of my conf file below. Are there
any adjustments I can make to the parameters that might help fix my problem?

Thank you!

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters
 /home/athenax/scratch-midway2/chainA-open-ins1-gbis-run2/files/par_all36_prot.prm
parameters
 /home/athenax/scratch-midway2/chainA-open-ins1-gbis-run2/files/toppar_water_ions_esmael.str

# Implicit Solvent
gbis on
alphaCutoff 12.0
ionConcentration 0.3

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 14.0
switching on
switchdist 13.0
pairlistdist 16.0

# Integrator Parameters
timestep 2.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on
langevinDamping 1
langevinTemp $temperature
langevinHydrogen off

# Output
outputName $outputname
restartfreq 500
dcdfreq 1000
xstFreq 250
outputEnergies 100
outputPressure 100

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