LangevinTemp and KE calculation

From: E. Prabhu Raman (eraman_at_gmu.edu)
Date: Tue Jul 15 2008 - 18:25:49 CDT

Hi All,
I intend to obtain NVT sampling of a test system (protein+water = 2422 Atoms) and am using Langevin Dynamics to maintain temperature(300 K).
The Configuration file is here:
http://binf.gmu.edu/eraman/downloads/val_sample.namd

There is inconsistency in the Kinetic Energy value and TEMP (which I believe is instantaneous) in the output file. I do know that due to finite system size the instantaneous Temp will not be equal to the intended Temp, but this error is in the calculation of instantaneous value itself.

K.E = 3/2 NkT

Take for example the output record at the end of this email and plug in values(I convert kcal/mol to J/mol):
1480.6935*4184 != 3/2 * 2422 * 8.31 * 305.6271

Using the same units and constants I do not get such error when I checked an NVE simulation which I did a couple of years ago.

ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 95000 12.9080 38.9750 13.8601 3.7679 -8377.0229 764.2146 1.3920 0.0000 1480.6935 -6061.2119 305.6271 -6061.5007 -6059.6038 303.7888 -825.1569 -825.0236 25412.1840 -1163.0572 -1161.2914

Can anyone point the error that I am commiting?
Thanks
Prabhu

E.Prabhu Raman
Ph.D Student, Bioinformatics & Computational Biology
George Mason University

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:39 CST