[gmx-users] CG energy minimization

[Justin A. Lemkul]

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
> > > _______________________________________________
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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>
> >
>
>
>
> --
> 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
>



========================================

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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