From: Fangqiang Zhu (fzhu_at_ks.uiuc.edu)
Date: Sat Nov 29 2003 - 00:34:30 CST
Hi,
This is because the external pulling forces do work to your system, and part of
the
work is irreversible and is converted to heat. As a result, the temperature will
increase
during the pulling.
Zhu
taeho.kim_at_utoronto.ca wrote:
> 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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