as Thomas mentioned, you would have periodic conditions, so you don't want
ntp and you need ntb to be 1 or something of that sort. Also, since you no
longer have PME for long range nonbonded forces, you'll need to increase
cut to something such that all nonbonded interactions are directly
calculated (like 999).
~Aron
On Wed, Apr 3, 2013 at 6:26 AM, Gaurao Dhoke
<g.dhoke.biotec.rwth-aachen.de>wrote:
> Hi,
> Thanks for your reply.
> The question is why I am working with vacuum because I want to know the
> effect of water solvent on protein molecule. So for comparison purpose I am
> doing both 1st in vacuum and then with water.
> If you have any better view about the same please let me know.
>
> -----Original Message-----
> From: steinbrt.rci.rutgers.edu [mailto:steinbrt.rci.rutgers.edu]
> Sent: 03 April 2013 12:17
> To: AMBER Mailing List
> Subject: Re: [AMBER] Regarding MD run in vacuum
>
> Hi,
>
> when you run a system in vacuum, you do not need to conduct a density
> equilibration. Your system does not have a simulation box, so ntb (and
> ntp) need to be set accordingly. The heating phase can be run as usual.
>
> However, the much more important question is why you would need to conduct
> a
> vacuum simulation. Force fields are not calibrated for these environments
> and most macromolecules are not stable without solvent. There is no
> tutorial
> for vacuum simulations because they constitute a special case that does not
> come up during typical simulation projects.
>
> Kind Regards,
>
> Thomas
>
> On Wed, April 3, 2013 4:56 am, Gaurao Dhoke wrote:
> > Hi,
> >
> > I read AMBER tutorial but I am not getting the exact procedure how to
> > run MD in vacuum. Is there necessity to involved all the steps that we
> > suppose to involved in normal MD run like heat.in, dens.in, equ.in
> >
> > I did the same thing as that of the normal MD run but without
> > solvating the complex. During density it is showing the error box not
> > found (peek ewald inpcrd:Box info not found in inpcrd).
> >
> > Can anyone suggest me the steps and what to do exactly.
> >
> >
> >
> > Thank in advance
> >
> >
> >
> > ------------------------------------------------------
> >
> > Gaurao Dhoke
> >
> > M.S. (Pharm.) Pharmacoinformatics
> >
> > PhD. Student
> >
> >
> >
> > Department of Biotechnology
> > RWTH Aachen University
> > Worringerweg 1
> > 52074 Aachen
> > Germany
> >
> >
> >
> > Phone: +49-241-80-26628
> >
> > E-mail: <mailto:g.dhoke.biotec.rwth-aachen.de>
> > g.dhoke.biotec.rwth-aachen.de
> >
> > Homepage: <http://www.biotec.rwth-aachen.de> www.biotec.rwth-aachen.de
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Apr 03 2013 - 07:00:06 PDT
