From: Pijush Ghosh (pijush.ghosh_at_ndsu.edu)
Date: Tue May 30 2006 - 12:04:34 CDT
Hello Sterling
Thank you for your response. So in NVE although theoretically those two
should be equal but actually they wont be because of the use of thermostat.
What is the case in NPT? Where should the major loss be you think?
Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA
Phone:
701-231-6491(Lab)
701-231-4341(Res)
-----Original Message-----
From: Sterling Paramore [mailto:paramore_at_hec.utah.edu]
Sent: Tuesday, May 30, 2006 11:47 AM
To: Pijush Ghosh
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: SMD Energy
If you're doing NVE dynamics, then yes. However, since you're most
likely using a thermostat, some of the work done on the system gets
converted into heat which is then transferred to the thermostat degrees
of freedom.
-Sterling
Pijush Ghosh wrote:
> Dear SMD Experts
>
> In NAMD and from concept of statistical mechanics is it logical to
> conclude that the area under the Force-Displacement curve for a
> protein is equal to the difference in the initial (t=0) and final
> (t=T) total energy(bonded + nonbonded) ?
>
>
>
> I would appreciate any discussion on this.
>
>
>
> Pijush Ghosh
>
> PhD Student
>
> Department of Civil Engineering
>
> North Dakota State University
>
> Fargo. ND. 58105. USA
>
> Phone:
>
> 701-231-6491(Lab)
>
> 701-231-4341(Res)
>
>
>
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