AMBER Archive (2006)

Subject: AMBER: density

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Mon May 15 2006 - 23:02:51 CDT

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

email mathew_kvarghese_at_yahoo.co.in

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