[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0
Alan
alanwilter at gmail.com
Tue Oct 27 15:20:46 CET 2015
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
> > > > --
> > > > Gromacs Users mailing list
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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
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