From: charlie (chengchangli123_at_163.com)
Date: Wed Jan 05 2011 - 02:07:48 CST
Hello , users
I run 500000 steps , then 300000 steps .But as can be seen below, the force is not continuous between the first run and the restart.
SMDTITLE: TS CURRENT_POSITION FORCE
SMD 500000 25.8631 33.7159 25.5426 -96.3874 265.343 285.517
SMDTITLE: TS CURRENT_POSITION FORCE
SMD 0 26.4281 34.7389 24.6329 1058.71 -2914.5 -3136.08
What's the problem ? Thanks and best wishes.
My restart configure file is
#######configure file #######################################
set inputname smd
structure ionized.psf
coordinates ionized.ref
bincoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel
extendedSystem $inputname.restart.xsc
outputName smd_relay
set temperature 310
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 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Output
binaryoutput no
dcdfreq 500 ;# 500steps = every 1ps
outputEnergies 100
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile ionized.ref
fixedAtomsCol B
}
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)
SMD on
SMDFile ionized.ref
SMDk 7
SMDVel 0.00002
SMDDir -0.24005720076537967 0.6608481549127442 0.7110922981646699
SMDOutputFreq 500
run 300000
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