AMBER Archive (2006)

Subject: RE: AMBER: density

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Tue May 16 2006 - 23:09:17 CDT

Hello Duan,

Thanks for your reply,

I have minimized the system first and the
equilibration run is done in a number of steps. First
the system is heated from 0 to 300 in constant volume
and 50 ps equilibration at constatnt pressure. Again a
number of simulations is done at constant volume,
gradually reducing the restraints. Then unrestrained
production run is done in NVE ensemble.

One of the output file is attached.
 the last lines of the restart files are

last line of first restart file(sl_md1.rst)

55.2371396 55.2371396 55.2371396 109.4712190
109.4712190 109.4712190

last line of second restart file - at constant
pressure(sl_md2.rst)

52.2594671 52.2594671 52.2594671 109.4712190
109.4712190 109.4712190

last line of last restart file(sl_md25.rst)

52.2594671 52.2594671 52.2594671 109.4712190
109.4712190 109.4712190

--- Yong Duan <duan_at_ucdavis.edu> wrote:

>
> 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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/\/\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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