Vlad,
Thanks for the advice. I'll re-run one of my sims to see the effect.
Chris
On 4/10/07, Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de> wrote:
>
> 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.eml-r.villa-bosch.de
> > <mailto:Vlad.Cojocaru.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.scripps.edu
> > <mailto:case.scripps.edu>
> > > <mailto:case.scripps.edu <mailto:case.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/
>
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> 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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Received on Wed Apr 11 2007 - 06:07:41 PDT
