From: taeho.kim_at_utoronto.ca
Date: Fri Nov 28 2003 - 17:53:27 CST
Hi
I followed SMD tutorial for Ubiqutine molecule and realized Temperature(TEMAVG
in log file) is getting higher. I got the following from the log file.
ENERGY: TS TEMAVG
SMD
0 315.1040
100 343.5757
600 388.5298
4000 414.5304
....
How can I explain this ?
I add part of conf file for your review.. Thanks,
Taeho
-------- conf ...
structure ../common/ubq.psf
coordinates ../common/ubq_ww_eq.pdb
outputName ubq_ww_pcv
set temperature 310
temperature $temperature
# Constant Temperature Control
langevin off ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
fixedAtoms on
fixedAtomsFile ../common/ubq_ww_eq.ref
fixedAtomsCol B
SMD on
SMDFile ../common/ubq_ww_eq.ref
SMDk 7
SMDVel 0.002
SMDDir 0.3524 0.4021 0.845
SMDOutputFreq 10
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