AMBER Archive (2006)

Subject: RE: AMBER: density

From: Yong Duan (duan_at_ucdavis.edu)
Date: Tue May 16 2006 - 00:37:28 CDT

Sounds like you were somehow doing NPE simulations. Can you send the output
file, instead, if it is not too large, and the last line of the beginning
and end restart files?

yong

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of mathew k varghese
> Sent: Monday, May 15, 2006 9:03 PM
> To: amber_at_scripps.edu
> Subject: AMBER: density
>
>
> Hello AMBER community,
>
> I have performed an explicit solvent simulation of an
> rna duplex in NVE ensemble.When I analysed the output
> files using process_mdout.perl the total energy,
> potential energy and temperature are stabilized. But
> the density is found to be increasing. I dont
> understand why it happens.
> the summmary.DENSITYfile and my input for production
> run are attached. Please look into them and help me.
> Thanks in advance
>
> Mathew
>
> /\/\athew
>
> Mathew K Varghese
> Research Scholar
> School of Pure and Applied Physics
> M.G.University
> Kottayam, Kerala
> India
>

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