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
>
>
>
>
>
>
>
> _______________________________________________
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> 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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Received on Wed Apr 03 2013 - 03:30:03 PDT
