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@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@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
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