[gmx-users] MD run with position restraints

[David]

On Fri, 2005-09-23 at 10:10 -0700, Gia Maisuradze wrote:
> Thanks for the web-site, there are a lot of interesting stuff there. 
> However, I could not find the answer on my question. MD run with position 
> restraints should be shorter than full run, but it is not clear for me how 
> short. I am going to run long 100ns MD simulation. How long should I run MD 
> with position restraints?
It's up to you to decide. A couple of 10s of ps usually is sufficient.
Check energy and density convergence.
> 
> Thanks in advance,
> 
> Gia
> 
> ----- Original Message ----- 
> From: <leafyoung81-group at yahoo.com>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Thursday, September 22, 2005 6:24 PM
> Subject: Re: [gmx-users] MD run with position restraints
> 
> 
> --- Gia Maisuradze <gia at chem.unr.edu> wrote:
> 
> > Hi,
> >
> > I am going to run long MD simulation (100ns).
> > According to manuel first I
> > should run MD with position restraints and then full
> > MD run without
> > restraints. I was wondering how many nanosecond MD
> > run with restraints I
> > should perform in my case.
> http://indigo1.biop.ox.ac.uk/MD_workshops/equilibrium.pdf
> >
> > Thanks in advance,
> >
> > Gia Maisuradze
> >
> >
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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