AMBER Archive (2006)

Subject: RE: AMBER: density

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Wed May 17 2006 - 22:24:07 CDT

Hello Ross,

Thanks for clarifying my problem. I have just used the
process_mdout.perl script and plotted the
summary.DENSITY using xmgrace. In the graph it is
found that the density is go on increasing.
Actually I dont want to calculate density. I just want
to verfy that whether there is any problem with my
simulation.

Thanking you,

Mathew
--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:-
> ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on
> request |
>
> Note: Electronic Mail is not secure, has no
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> be read every day, and should not be used for urgent
> or sensitive issues.
>
> > -----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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/\/\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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