[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

Mark Abraham mark.j.abraham at gmail.com
Tue Oct 27 15:59:51 CET 2015


Hi,

No, your old calculation used to work because you specified pbc = no. The
defaults in GROMACS have ~always included pbc = yes and cutoffs of 1nm, so
grompp -c single-atom-with-no-box.pdb -f just-steep.mdp has never worked.
Simply specifying pbc = no doesn't work in the Verlet scheme (which is the
default in 5.1) because that combination is not supported (yet, but it will
be). So, currently there's an implicit requirement that the box size is
large enough for the Verlet-scheme defaults. So Alan can put his single
molecule in a 3nm box with editconf and you will likely have no problems in
future :-)

There's no intention to make an ~empty .mdp file actually work with any
possible input configuration, because I suspect that would require writing
code that would be useless, or making something have a default that was
less than useful.

If you want an .mdp file with all the current defaults, you can inspect
mdout.mdp after

touch input.mdp
grompp -c something -f input -p something

Mark

On Tue, Oct 27, 2015 at 3:21 PM Alan <alanwilter at gmail.com> wrote:

> Thanks Victor,
>
> My system is the simplest you can think. It’s just one molecule, say in
> vacum, and I just want to check if the topology is OK for GMX, run a single
> point energy calculation. This always used to work, but apparently now that
> Verlet is default, it looks like I can’t use my yesteryear approach. So,
> which minimum parameters do I have to define to run an EM using
> steep-descent with 500 iters?
>
> Alan
>
> On 27 October 2015 at 13:38, Victor Rosas Garcia <rosas.victor at gmail.com>
> wrote:
>
> > As I understand it, this error is not dependent on the mdp file, but on
> > your system. Maybe you need to define a larger system.  Of course, you
> > could try decreasing rlist, but the value of rlist is usually dependent
> on
> > the force field you are using, so you risk breaking the physics if you
> > decrease rlist just to make the simulation work.
> >
> > Hope this helps
> >
> > Victor
> >
> > 2015-10-27 7:02 GMT-06:00 Alan <alanwilter at gmail.com>:
> >
> > > Dear Mark, the simple
> > > em.mdp:
> > > integrator               = steep
> > > nsteps                   = 500
> > >
> > > does not work anymore with GMX 5.1.
> > >
> > >   ERROR: The cut-off length is longer than half the shortest box vector
> > or
> > >   longer than the smallest box diagonal element. Increase the box size
> or
> > >   decrease rlist.
> > >
> > > How to make it work again and still keep the em.mdp the smallest,
> > simplest
> > > possible?
> > >
> > > Thanks,
> > >
> > > Alan
> > >
> > > On 27 August 2014 at 17:09, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> > >
> > > > You only need the integrator :-) Default for everything else works.
> > > >
> > > > Mark
> > > > On Aug 27, 2014 4:24 PM, "Alan" <alanwilter at gmail.com> wrote:
> > > >
> > > > > Hi there,
> > > > >
> > > > > I need a very simple em.mdp and md.mdp, to simply test my generated
> > GMX
> > > > > files from ACPYPE.
> > > > >
> > > > > It contains just a single small molecule without solvent. I just
> need
> > > to
> > > > > test if the topology file is OK (i.e. if grompp and mdrun will
> accept
> > > > it),
> > > > > so I used to use these parameters with GMX 4:
> > > > >
> > > > > em.mdp:
> > > > > cpp                      = /usr/bin/cpp
> > > > > define                   = -DFLEXIBLE
> > > > > integrator               = steep
> > > > > nsteps                   = 500
> > > > > constraints              = none
> > > > > emtol                    = 1000.0
> > > > > emstep                   = 0.01
> > > > > nstcomm                  = 1
> > > > > ns_type                  = simple
> > > > > nstlist                  = 0
> > > > > rlist                    = 0
> > > > > rcoulomb                 = 0
> > > > > rvdw                     = 0
> > > > > Tcoupl                   = no
> > > > > Pcoupl                   = no
> > > > > gen_vel                  = no
> > > > > nstxout                  = 1
> > > > > pbc                      = no
> > > > >
> > > > > md.mdp:
> > > > > cpp                      = /usr/bin/cpp
> > > > > define                   = ;-DFLEXIBLE
> > > > > integrator               = md
> > > > > nsteps                   = 500
> > > > > constraints              = none
> > > > > emtol                    = 1000.0
> > > > > emstep                   = 0.01
> > > > > comm_mode                = angular
> > > > > ns_type                  = simple
> > > > > nstlist                  = 0
> > > > > rlist                    = 0
> > > > > rcoulomb                 = 0
> > > > > rvdw                     = 0
> > > > > Tcoupl                   = no
> > > > > Pcoupl                   = no
> > > > > gen_vel                  = no
> > > > > nstxout                  = 1
> > > > > pbc                      = no
> > > > >
> > > > > But these parameters won’t work anymore with GMX 5. Can someone
> > suggest
> > > > me
> > > > > the minimum alterations or completely new values so I could run a
> > quick
> > > > EM
> > > > > and MD? And if they were compatible to both GMX 4 and 5 that’d be
> > > great.
> > > > >
> > > > > Many thanks in advance,
> > > > >
> > > > > Alan
> > > > >
> > > > >
> > > > > --
> > > > > Alan Wilter SOUSA da SILVA, DSc
> > > > > Bioinformatician, UniProt
> > > > > European Bioinformatics Institute (EMBL-EBI)
> > > > > European Molecular Biology Laboratory
> > > > > Wellcome Trust Genome Campus
> > > > > Hinxton
> > > > > Cambridge CB10 1SD
> > > > > United Kingdom
> > > > > Tel: +44 (0)1223 494588
> > > > > --
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> > >
> > > --
> > > Alan Wilter SOUSA da SILVA, DSc
> > > Senior Bioinformatician, UniProt
> > > European Bioinformatics Institute (EMBL-EBI)
> > > European Molecular Biology Laboratory
> > > Wellcome Trust Genome Campus
> > > Hinxton
> > > Cambridge CB10 1SD
> > > United Kingdom
> > > Tel: +44 (0)1223 494588
> > > --
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>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
> --
> Gromacs Users mailing list
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> posting!
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