[gmx-users] Single or Double precision

[Mark Abraham]

Yes, although the mismatch will typically be noted in the output.

Mark


On Mon, Feb 24, 2014 at 1:30 PM, Mostafa Javaheri <m.javaheri at gu.ac.ir>wrote:

> Dear Justin
> I minimized and equilibrated (em, nvt and npt) my protein by the
> single-precision GROMACS 4.5.3 version and then made final mdrun.tpr by the
> following command:
> "grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
> mdrun.tpr"
> Could I run final simulation of the mdrun.tpr file on the other server
> which double-precision GROMACS 4.5.3 version is installed? or vice versa?
> Sincerely
> M.Javaheri
>
>
> On Sat, 02/01/2014 04:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> > On 1/31/14, 11:53 AM, Mostafa Javaheri wrote:
> > > Dear Justin
> > >
> > > I have a problem with centering the hetrodimer protein in the
> dodecahedron or
> > > octahedron box, the related commands are:
> > >
> > > 1.pdb2gmx -f A1CBIII-W3.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb
> > > -nochargegrp -merge all -posrefc 1000 -renum
> > >
> > > 2.editconf -f conf.pdb -o boxed.pdb -c -d 1.0 -bt dodecahedron
> > >
> > > 3.genbox -cs -cp boxed.pdb -o solvated.pdb -p topol.top
> > >
> > > in the solvated.pdb output file protein represents at the corner of
> the box and
> > > some of it is out of box although it will not happen for -bt cubic
> (whole
> > > protein will be centered in the box), considering periodic boundary
> condition,
> > > mdrun will be ok; after five ns mdrun one of the protein's chain
> represents
> > > inside the box and the other chain out of the box in md.gro file.
> After running
> > > trjcov several times with different options (including -pbc mol, atom,
> nojump,
> > > whole -center, -ur compact) none of them could put the whole protein
> in one unit
> > > cell. I would be grateful again for your help.
> >
> > Without seeing exactly what you've tried, it's rather futile to try to
> guess
> > what to suggest.  Complexes are difficult to deal with.  The first step
> should
> > almost always be trjconv -pbc nojump, but further iterations may vary.
>  See
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
> > and also be aware that you can (and should, in many cases) use custom
> index
> > groups for centering or other fitting, i.e. some residues at the
> protein-protein
> > interface or something else that makes sense.  Centering on "protein"
> normally
> > fails in such cases, for reasons discussed repeatedly in the list
> archive.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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