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> 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> 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>> 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
> >
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu <mailto:amber.scripps.edu>
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > <mailto:majordomo.scripps.edu>
> >
> >
>
> --
>
> ----------------------------------------------------------------------------
> 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
>
> ----------------------------------------------------------------------------
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Apr 11 2007 - 06:07:40 PDT
