Re: LangevinTemp and KE calculation

From: E. Prabhu Raman (eraman_at_gmu.edu)
Date: Wed Jul 16 2008 - 12:56:22 CDT

Dear Peter,

> did you properly take the fact that you're using rigidbonds into
> account? Every constrained bond removes one degree of freedom from
> your
> system...

Thanks for pointing that out. By subtracting the appropriate constrained degrees of freedom (number of Hydrogens bonded to heavy atoms and number of H-O-H angle constraints) I now get the correct computed instantaneous temperature from the KE.
Regards
Prabhu

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

----- Original Message -----
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
Date: Wednesday, July 16, 2008 7:53 am
Subject: Re: namd-l: LangevinTemp and KE calculation

> Dear Prabhu,
> did you properly take the fact that you're using rigidbonds into
> account? Every constrained bond removes one degree of freedom from
> your
> system...
>
> Best,
> Peter
>
> E. Prabhu Raman wrote:
> > 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
> >
>
>

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