[gmx-users] Re: Energy Minimization

[David]

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
> > >
> > > _______________________________________________
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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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> 
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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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