[gmx-users] CG energy minimization

[Myunggi Yi]

Yes, I did (constraints=none).

These are my conclusions.

Since I could do CG without my position restraint,
My .top doesn't include any constraint. (if my posre.itp is not constraint).
The manual says "SD is enough for general purpose".
If one wants to do energy minimization with position restraint, then do SD
only.

Thank you anyway.


On Jan 14, 2008 5:21 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> Perhaps this is too obvious to be the solution, but have you considered
> setting
> 'constraints = none' in your em.mdp file?  After all, as Mark originally
> pointed out, the documentation will tell you that constraints and CG don't
> mix.
>
> -Justin
>
> Quoting Myunggi Yi <myunggi at gmail.com>:
>
> > Sorry this is my top file.
> >
> > #include "ffgmx.itp"
> > #include "../lipid.popc.itp"
> > #include "popc.itp"
> > #include "pro.itp"
> > #include "ions.itp"
> > #include "spc.itp"
> >
> > Which one defines constraints?
> >
> >
> > On Jan 14, 2008 4:35 PM, Myunggi Yi <myunggi at gmail.com> wrote:
> >
> > > Thnak you.
> > >
> > > I don't use any constrant like lincs or shake.
> > > Why do I get the error message.
> > >
> > >
> > >
> > > On Jan 14, 2008 4:11 PM, Mark Abraham < Mark.Abraham at anu.edu.au>
> wrote:
> > >
> > > > Myunggi Yi wrote:
> > > > > Dear users,
> > > > >
> > > > > I'd like to restraint the protein during the minimization.
> > > > > I've got the following message.
> > > >
> > > > In GROMACS, restraints are different from constraints. Check out the
> > > > manual for details.
> > > >
> > > > > ERROR: can not do Conjugate Gradients with constraints
> > > >
> > > > Your .top is defining some constraints, and if you'd checked out the
> > > > manual, you'd have confirmed that GROMACS can't handle constraints
> with
> > > > the CG algorithm.
> > > >
> > > > > em.mdp file
> > > > > +++++++++++++++++++++
> > > > > cpp                      = cpp
> > > > > include                  =
> > > > > define                   = -DPOSRES
> > > > > define                   = -DFLEXIBLE
> > > > >
> > > > > ; RUN CONTROL PARAMETERS
> > > > > integrator               = cg
> > > > > ; Start time and timestep in ps
> > > > > tinit                    = 0
> > > > > dt                       = 0.001
> > > > > nsteps                   = 250
> > > > > +++++++++++++++++++++
> > > > >
> > > > > How can I do this?
> > > >
> > > > Either don't use constraints or don't use CG.
> > > >
> > > > Mark
> > > > _______________________________________________
> > > > gmx-users mailing list     gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive at http://www.gromacs.org/search before
> > > > posting!
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> > > >
> > >
> > >
> > >
> > > --
> > > Best wishes,
> > >
> > > MYUNGGI YI
> > > ==================================
> > > KLB 419
> > > Institute of Molecular Biophysics
> > > Florida State University
> > > Tallahassee, FL 32306
> > >
> > > Office: (850) 645-1334
> > > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi> <
> http://www.scs.fsu.edu/%7Emyunggi>
> > >
> >
> >
> >
> > --
> > Best wishes,
> >
> > MYUNGGI YI
> > ==================================
> > KLB 419
> > Institute of Molecular Biophysics
> > Florida State University
> > Tallahassee, FL 32306
> >
> > Office: (850) 645-1334
> > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi>
> >
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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