From: hl332_at_drexel.edu
Date: Tue Mar 13 2007 - 14:06:07 CDT
Hi all,
I have been doing an NVT equilibration run followed by an NVE production run (both in a water sphere with spherical B.C.) where i take restart coordinate,vel and extended system for NVE run from NVT simulation.
During NVE run, i notice two strange things: One is that protein is spinning unlike NVT equil. run where it was vibrating without any C.O.M motion. Here C.O.M is moving and after a few nanoseconds, continuing spinning protein goes to one boundary. Second thing, energy (TOTAL3 in Log)can be seen increasing with ana average ~3kal/mol per ns. My question is why this thing is spinning and why total energy is not constant. My config file is given below:
Thanks in advance..
===========================
structure phecal_ion.psf
coordinates phecal_ion.pdb
set outputname mainrun
# Continuing a job from the restart files
set inputname equil.restart
binCoordinates $inputname.coor
binVelocities $inputname.vel ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.xsc
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 1.0
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Output
outputName $outputname
restartfreq 500
dcdfreq 5000
outputEnergies 500
outputPressure 500
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 0.463018612372 -1.61382842129 -14.3611089107
sphericalBCr1 41.0
sphericalBCk1 10
sphericalBCexp1 2
#############################################################
## EXECUTION SCRIPT ##
###########################################################
run 20000000 ;# 20ns because 1fs time step gives 10,00,000 steps for 1ns
=======================
------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823
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