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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 03 2013 - 03:30:04 PDT
