Protein trapped on an edge of the simulation cell using C36 force field

Date: Tue Jul 11 2017 - 03:15:51 CDT

Dear namd mailing list,

I used the par_all36m_prot.prm file to simulate a protein in NVT with
PBC, PME, Langevin thermostat with TIP3 explicit solvent.
Strangely enough, after about 60 ns the protein gets "trapped" on an
edge of the simulation cell with almost zero translation and rotation.
Since I didn't observe in the past a similar behavior using the 27
force field for proteins and nucleic acids, I wonder if this could be
attributed to the C36 force field. Does anybody have a similar

Below is a part of my configuration file

# Continuing a job from the restart files
if {1} {
set inputname eq_NVT_C36_4
binCoordinates $inputname.restart.coor
#binVelocities $inputname.restart.vel
extendedSystem $inputname.restart.xsc

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

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