AMBER Archive (2007)

Subject: AMBER: Re: Calculating Energies with imin=5

From: Pavan G (pavanamber_at_gmail.com)
Date: Fri Nov 30 2007 - 06:24:18 CST

Hello All,

>
> I heated water from 50 to 200K in a 100ps long simulation in a NPT
> ensemble. I then used ptraj to process the raw trajectory(1) ensuring that
> the output was in a periodic box(2). I then used
> ---------------
> test sander
> &cntrl
> imin = 5,
> maxcyc = 1,
> ntpr = 1,
> ntwx=1,
> /
> ------------------
> to get energies using sander and the imaged trajectory(2). Both original
> and imin=5 output files are here:

http://compbio.ornl.gov/~pkc/ <http://compbio.ornl.gov/%7Epkc/plot.jpg>
sander-original.out
http://compbio.ornl.gov/~pkc/ <http://compbio.ornl.gov/%7Epkc/plot.jpg>
sander-imin-5.out

> The energies looked like this http://compbio.ornl.gov/~pkc/plot.jpg>. Could somebody comment on the discrepancy? For those who cannot access the
> figure, the sander-original energy data reaches -3700 Kcal/mol while the
> data from imin=5 reached -3300 Kcal/mol.
>
> Thanks
> Pavan Ghatty
>

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