From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Mon Aug 30 2004 - 13:12:17 CDT
I believe one of the NAMD summer school tutorials has an example of
calculating the temperature from your MD data using the MB distribution.
I'd suggest you check your proceedure against the one listed in that
tutorial if you haven't already.
On Mon, 30 Aug 2004, Raymond C. Fort Jr. wrote:
> We are running a simulation with the temperature set to 310 K in the NPT
> regime. After about 500 ps, the system apparently reaches equilibrium,
> with the backbone rmsd and the temperature from the Maxwell-Boltzman
> analysis both becoming constant. However, the temperature from M-B comes
> out 190 K.
> Clearly, we're doing something wrong. Any suggestions?
> Professor Ray Fort Jr. rcfort_at_maine.edu
> Department of Chemistry chemistry.umeche.maine.edu/fort.html
> University of Maine Voice: (207)-581-1180
> Orono, ME 04469 FAX: (207)-581-1191
> Computer modeling of organic and biomolecules; chemistry of lignin
> and cellulose
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