[gmx-users] Velocity units

[Jordi Camps]

Hello,

Which are the units used to express the velocities in .gro files? Nm/ps? I
cannot find this data anywhere :-(

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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