[gmx-users] Energy minimisation

[Justin A. Lemkul]

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> Quoting JMandumpal <jesbman at rediffmail.com>:
>
> > Dear Justin,
> >
> > Thanks for the response.
> >
> >
> > This is my input file (em.mdp) which contains parameters for doing energy
> > minimisation.
> >
> >  cpp            = /lib/cpp
> > define         = -DPOSRES -DFLEX_
> > constraints    =  none
> > morse          =  no
> > integrator     = steep
> > nsteps         = 2000
> > ; Energy minimizing
> > emtol          = 100
> > emstep         = 0.00001
> > nstcomm        = 1
> > ns_type        = grid
> > rlist          = 1.0
> > rcoulomb       = 1.0
> > rvdw           = 1.0
> > Tcoupl         = no
> > Pcoupl         = no
> >
> >
> >
> > MY BOX DIMENSION, 20.1* 20.1* 20.1 ANGSTROM.
>
> And that's why grompp is complaining.  Your cutoff is 1.0 nm, which is half
> of
> your box size.  You said you tried decreasing  your cutoff?  To what value?
>
> Also note that -DFLEX_ is not a valid definition, unless you've created it
> yourself.  What you probably want (from the thread) is -DFLEX_SPC.
>
> -Justin
>
> >
> >
> > THIS IS THE THREAD WHERE I COLLECTED THE .mdp FILE FOR ENERGY MINIMISATION.
> >
> > http://www.gromacs.org/component/option,com_wrapper/Itemid,84/
> >
> >
> >
> >
> >
> > regards
> > Jestin
>
>
>
> ========================================
>
> 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/
>
> ========================================



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

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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