restarting heating protocol problem:

From: Parminder Mankoo (pkmankoo_at_gmail.com)
Date: Tue Sep 23 2008 - 12:47:42 CDT

Hello,

I am trying to run a restart of heating in NAMD. My first run stopped at
20,000 step with temp=199.937K. I used the following conf file for restart,
by using bincoor and binvelocities.
But the first output it prints in the log file is:
"REASSIGNING VELOCITIES AT STEP 20000 TO 300 KELVIN
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 20000 3121.5677 9762.5466 7318.4962
545.8575 -1214118.6359 144479.6058 1267.4101 0.0000
185224.4693 -862398.6828 300.1631 -862296.7986
-862296.7986 300.1631 420.8836 496.8736
3278600.0000 420.8836 496.873"
Shouldn't the first temp be 199.937K since that's what the vel and
reassigntemp are telling it to be. It should start the same heating protocol
from 199.937K to 300K instead of reassigning straight o 300K. Please let me
know what I am doing wrong?

Thanks,
Parminder
__________________________
structure prot.psf
Coordinates minicl30prot.coor

bincoordinates heat2cl30prot.coor
binvelocities heat2cl30prot.vel

extendedSystem heat2cl30prot.xsc

paraTypeXplor off
paratypecharmm on
parameters par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0

switching on
switchdist 10
cutoff 13
pairlistdist 14
margin 2.5

PME on
PMEGridSizeX 196 #EDIT THIS!
PMEGridSizeY 128 #EDIT THIS!
PMEGridSizeZ 128 #EDIT THIS!

cellBasisVector1 194.0000 0 0 #EDIT THIS!
cellBasisVector2 0 130.0000 0 #EDIT THIS!
cellBasisVector3 0 0 130.0000 #EDIT THIS!
cellOrigin 0.0 0.0 0.0 #EDIT THIS!

# Integrator Parameters
timestep 1.0
rigidBonds all
rigidTolerance 1.0e-6
useSettle on
nonbondedFreq 1
fullElectFrequency 4
stepspercycle 20

wrapWater on
#wrapAll on

binaryoutput no
restartname heat2-1cl30prot #EDIT THIS if you need!
outputname heat2-1cl30prot #EDIT THIS! - your output
filename
restartfreq 1000 # 5000steps = every 7.5ps
dcdfreq 1000
xstFreq 1000
outputEnergies 500
outputPressure 500
outputTiming 1000

#temperature 199.9370
seed 1010

firsttimestep 20000
numsteps 30000

minimization off

constraints on
consref minicl30prot.coor
conskfile prot-cl-30.pdb
conskcol B

reassignTemp 199.9370
reassignFreq 1
reassignIncr .01
reassignHold 300

numAtomsSelf 88
numAtomsPair 140

twoAwayX yes # when #atoms/#cpus < 200
twoAwayY yes # when #atoms/#cpus < 50
twoAwayZ yes # when #atoms/#cpus < 20

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