AMBER Archive (2007)

Subject: Re: AMBER: Constant volume simulations

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Apr 10 2007 - 11:02:42 CDT

Chris,

ntwx sets the frquency of trajectory frame output ... For a 1.000.000
steps simulation I usually use 500 and if later I dont need so many
frames, I post process the trajectory with ptraj ...
However .. of course there is always the question ... how much storage
space you have ....

10.000 steps for 1 frame means 20 ps .... you might lose some important
information by having such a big time/frame (but of course this also
depends on what you want to see) .....

I would generally say that if you have storage place, it doesnt harm to
have more trajectory frames ... If you dont need then you always have
the option to remove them, with ptraj or other analysis soft ...

cheers
vlad

Christopher Gaughan wrote:

> Vlad,
>
> I am relatively new to MD- what value of ntwx would you recommend?
>
> Chris
>
>
> On 4/10/07, *Vlad Cojocaru* < Vlad.Cojocaru_at_eml-r.villa-bosch.de
> <mailto:Vlad.Cojocaru_at_eml-r.villa-bosch.de>> wrote:
>
> Christopher,
>
> Your system is not expanding ... Its just that the waters move out of
> the primary box .... What you see is actually very normal. In order to
> see your original box you need to image back to the primary box.
> Usually
> I do that with ptraj postprocessing (see the image and center
> command in
> ptraj) ...
>
> cheers
> vlad
>
> P.S. Isn't 10.000 a too large value for ntwx for a 1.000.000 steps
> simulation ???
>
>
> Christopher Gaughan wrote:
>
> > here is my md.in <http://md.in> <http://md.in> file:
> >
> > &cntrl
> > imin = 0, nmropt = 0,
> >
> > ntx = 1, irest = 0, ntrx = 1,
> >
> > ntxo = 1, ntpr = 10000,
> > ntwr = 50,
> > ntwx = 10000, ntwv = 0, ntwe = 0,
> > ioutfm = 0, ntwprt = 0,
> >
> > ntf = 2, ntb = 1, dielc = 1.0,
> > scnb = 2.0, scee = 1.2
> >
> > ibelly = 0, ntr = 0,
> >
> > nstlim = 1000000,
> > dt = 0.002, pres0 = 1,
> > temp0 = 300.00, tempi = 300.0, ig = 71277,
> > ntt = 1,
> > tautp = 1.0, vlimit = 0.0, ntp = 0,
> >
> > ntc = 2, tol = 0.00005,
> >
> > //
> >
> > However, I have erred in that the output from amber does not
> show that
> > the volume is increasing (it shows no values for each time
> point). The
> > problem arises when I view my trajectory in VMD 1.8.5- The waters,
> > which initially start out as a box around my peptide, appear to to
> > just expand out throughout the simulation.
> >
> > I am not sure if this is just a visualization problem inherent from
> > the use of periodic boundary conditions (however I use the periodic
> > box option in VMD) or whether the system is indeed expanding.
> >
> >
> >
> > On 4/9/07, * David A. Case* < case_at_scripps.edu
> <mailto:case_at_scripps.edu>
> > <mailto:case_at_scripps.edu <mailto:case_at_scripps.edu>>> wrote:
> >
> > On Mon, Apr 09, 2007, Christopher Gaughan wrote:
> > >
> > > I am running simulations in Amber 8 using N V T ensemble.
> > However, when I
> > > track the volume during the MD runs I notice that it keeps
> > increasing
> > > throughout the simulation.
> >
> >
> > We need more information. You are obviously not doing a
> constant
> > volume
> > simulation. But all you have said so far is what you *intended*
> > to do, not
> > what you actually did (i.e. not your input). Be sure to
> check the
> > value of
> > ntp.
> >
> >
> > .....dac
> >
> >
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> >
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de <http://r.villa-bosch.de>
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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