[gmx-users] Velocity units
David
spoel at xray.bmc.uu.se
Tue May 24 17:31:49 CEST 2005
On Tue, 2005-05-24 at 17:04 +0200, Jordi Camps wrote:
> Hello,
>
> Which are the units used to express the velocities in .gro files? Nm/ps? I
> cannot find this data anywhere :-(
>
Correct. Chapter 2 in the manual.
> Thank you,
>
> --
>
> Jordi Camps Puchades
>
> Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> UPC-CIRI
> c/. Jordi Girona 1-3
> Modul C6-E201 Tel. : 934 011 650
> E-08034 Barcelona Fax : 934 017 014
> Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
>
> > -----Mensaje original-----
> > De: gmx-users-bounces at gromacs.org
> > [mailto:gmx-users-bounces at gromacs.org] En nombre de Jordi Camps
> > Enviado el: lunes, 23 de mayo de 2005 17:33
> > Para: 'Discussion list for GROMACS users'
> > Asunto: RE: [gmx-users] Excessive compute time using PME
> >
> > Hello,
> >
> > I started with a EM and a slightly bigger box (5% bigger).
> > But some problem
> > remains:
> > Steepest Descents:
> > Tolerance (Fmax) = 1.00000e+03
> > Number of steps = 500
> > Fatal error: ci = -2147483648 should be in 0 .. 2001
> > [FILE nsgrid.c, LINE 218]
> >
> > Where is supposed to be the center of the box? Because in the
> > the file, only the vectors are given, but no reference point.
> >
> > Thanks!
> >
> > --
> >
> > Jordi Camps Puchades
> >
> > Instituto Nacional de Bioinformatica (INB) Nodo Computacional
> > GNHC-2 UPC-CIRI c/. Jordi Girona 1-3
> > Modul C6-E201 Tel. : 934 011 650
> > E-08034 Barcelona Fax : 934 017 014
> > Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
> >
> > > -----Mensaje original-----
> > > De: gmx-users-bounces at gromacs.org
> > > [mailto:gmx-users-bounces at gromacs.org] En nombre de David van der
> > > Spoel Enviado el: jueves, 19 de mayo de 2005 14:31
> > > Para: Discussion list for GROMACS users
> > > Asunto: RE: [gmx-users] Excessive compute time using PME
> > >
> > > On Thu, 2005-05-19 at 13:13 +0200, Jordi Camps wrote:
> > > > Hello,
> > > >
> > > > I have some news about the problem. Yesterday I saw that
> > the input
> > > > that I was feeding was not completely contained in the
> > > octahedron, so
> > > > I recentered the travelling waters and now I have a true
> > > octahedron as input for mdrun.
> > > > If I chech the coordinates of the tpr file (extracted with
> > > editconf) I
> > > > continue seeing an octahedron in VMD.
> > > > But when I run the simulation with mdrun, it fails. And
> > before core
> > > > dumping, mdrun writes two files: step-1.pdb and step0.pdb.
> > > > Step0.pdb shows an exploded molecule (and waters).
> > > > Step-1.pdb shows my input in cubic boundaries. I think
> > that this is
> > > > the problem. I'm feeding an octahedron and mdrun is
> > > interpreting this
> > > > like a box. There are some special considerations I should
> > > take into
> > > > account if I want to simulate with an octahedron? Perhaps
> > > I'm missing
> > > > some parameter in the grompp.mdp file? The box vectors,
> > > like the ones
> > > > that I have in the file, are 6.72730 6.34256 5.49282
> > > 0.00000 0.00000
> > > > 2.24243 0.00000 -2.24243 3.17128.
> > > >
> > > > Thank you for yout help.
> > > start with EM, if necessary with slightly larger box.
> > > >
> > > > Sincerely,
> > > >
> > > > --
> > > > Jordi Camps Puchades
> > > > Instituto Nacional de Bioinformatica (INB) Nodo
> > > Computacional GNHC-2
> > > > UPC-CIRI
> > > > c/. Jordi Girona 1-3
> > > > Modul C6-E201 Tel. : 934 011 650
> > > > E-08034 Barcelona Fax : 934 017 014
> > > > Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
> > > >
> > > > -----Mensaje original-----
> > > > De: gmx-users-bounces at gromacs.org
> > > > [mailto:gmx-users-bounces at gromacs.org] En nombre de Anton
> > Feenstra
> > > > Enviado el: jueves, 19 de mayo de 2005 7:45
> > > > Para: Discussion list for GROMACS users
> > > > Asunto: Re: [gmx-users] Excessive compute time using PME
> > > >
> > > >
> > > > Jordi Camps wrote:
> > > >
> > > > > Hello list!
> > > > >
> > > > > Yes, you were right on the problem. I computed bad box
> > > vectors which
> > > > > makes the box extra-large. Now I reduced the box to it's
> > > real size,
> > > > > but now I get some kind of error. GXM writes an
> > step-1.pdb and a
> > > > > step0.pdb files (the second one shows that all the molecules
> > > > > exploded) and core dumps. I'm working to find the cause.
> > > >
> > > > Loook at your periodic boundaries. If you changed the box
> > size, you
> > > > may well have (bad) overlap at the 'edges'.
> > > >
> > > >
> > > --
> > > David.
> > > ______________________________________________________________
> > > __________
> > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > > phone: 46 18 471 4205 fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se spoel at gromacs.org
> > > http://xray.bmc.uu.se/~spoel
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > ++++++++++
> > >
> > >
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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