[gmx-users] Re: Energy Minimization

[Gia Maisuradze]

David,

Yes, l-bfgs does better job than steep. I have checked it.

Thanks,

Gia Maisuradze

----- Original Message ----- 
From: "David" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, January 12, 2005 1:54 PM
Subject: Re: [gmx-users] Re: Energy Minimization


> On Wed, 2005-01-12 at 13:03 -0800, Gia Maisuradze wrote:
> > David,
> >
> > Thanks for your reply. Below I have attached the files for energy
> > minimization of Ribonuclease S-peptide, which is given in tutorial and I
> > followed exactly the tutrial "getting started". I have attached the file
how
>
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to Fmax < 2000 in 22 steps
> > Potential Energy  = -2.9970463e+04
> > Maximum force     =  1.9969060e+03 on atom 2437
> > Norm of force     =  4.9306812e+04
> This is good enough. When you do dynamics the energy will drop. Energy
> minimization , in particular with steep, is not good enough. l-bfgs
> might do a better job.
> >
> > gcq#270: "Live for Liposuction" (Robbie Williams)
> >
> > According to the tutorial the potential energy should be lower
than -35700
> > kJ/mol (-42 x 850), but my result is higher.
> >
> > The same kind of problem I had for lambda repressor.
> >
> > How can I fix this problem?
> >
> > With best wishes,
> >
> > Gia Maisuradze
> >
> > ----- Original Message ----- 
> > From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Sent: Tuesday, January 11, 2005 11:54 PM
> > Subject: Re: [gmx-users] Re: Energy Minimization
> >
> >
> > > On Tue, 2005-01-11 at 16:42 -0800, Gia Maisuradze wrote:
> > > > Hi,
> > > >
> > > > I am a new user of GROMACS. I have sent this message one week ago
but
> > > > did not get any answer. I am trying to run MD simulation of one of
the
> > > > proteins. I followed the "getting started" tutorial. My question is
> > > > about minimization of my system in solvent. According to the
tutorial
> > > > the minimization should be finished when either the minimization has
> > > > converged or a fixed number of steps has been performed. In my case
> > > > the minimization has converged before it reached the fixed number of
> > > > steps. But the potential energy after minimization IS NOT lower than
> > > > potential energy calculated by formula: -42(kJ/mole)xN (N is a
number
> > > > of SPC water molecules). What is the problem? How can I fix it? The
> > > > same problem I had for Ribonuclease S-peptide given in tutorial. As
I
> > > > heard the problem might be a precision. Am I correct? My
calculations
> > > > run in single precision, so I may need a double precision. But I
don't
> > > > know how to change the precision. Can anyone help me to change a
> > > > single precission to double precision? Is there any other ways to
fix
> > > > this problem?
> > > Is the number of waters correct? It is not in the tutorial.
> > > >
> > > > My second question is about short and full MD run. According to the
> > > > tutorial to generate the input for the position restrained mdrun we
> > > > have the following command:
> > > >
> > > > grompp -f pr -o pr -c after_em -r after_em -p speptide
> > > >
> > > > for full md to do the same thing we have the following command:
> > > >
> > > > grompp -v -f full -o full -c after_pr -p speptide
> > > >
> > > > We can see that full MD is quite similar to the restrained MD, but
> > > > there is a difference which makes impossible to run full MD without
> > > > restrained MD. In full MD we have "-c after_pr" which is an input
file
> > > > and "after_pr" can be obtained from short MD run. Is it correct that
> > > > we can't run full MD run without short MD or is there any other way
to
> > > > run directly full MD (for example, use the same files for full MD as
> > > > used for short MD)?
> > > If you don't do the PR you may end up with large forces due to the
newly
> > > added solvent which may disrupt your original structure. This is
usually
> > > not what you want, but that is for you to decide of course.
> > > >
> > > > I look forward to hearing your reply,
> > > >
> > > > With best wishes,
> > > >
> > > > Gia Maisuradze
> > > >
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > -- 
> > > 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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> > >
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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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