AMBER Archive (2006)

Subject: RE: AMBER: density

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 17 2006 - 10:31:20 CDT

Hi Mathew,

In the constant volume calculations the density is not calculated and not
written to the output file. However if you are using my process_mdout.pl
script to extract information from the output file it extracts all potential
fields whether they are present in the output file or not. Thus if you are
running constant volume you will still get a density.dat file although it's
contents will be meaning less.

If you are not using this can you clarify what you mean by the density is
decreasing during the constant volume run? How are you calculating the
density?

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of mathew k varghese
> Sent: Tuesday, May 16, 2006 21:09
> To: amber_at_scripps.edu
> Subject: RE: AMBER: density
>
> 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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