[gmx-users] editconf

Nagy, Peter I. PNAGY at UTNet.UToledo.Edu
Mon Jul 14 19:13:01 CEST 2003

Dear Gromacs Users!

  I used the command editconf in order to orient my system in principal-
axis coordinate system.
  I typed:

editconf -f conf.gro -princ

and then got a strange out.gro file:

Great Red Owns Many ACres of Sand
    1ALA      N    1   2.899-36893488147419103000.000  -2.954
    1ALA     H1    2   2.894-36893488147419103000.000  -2.934
    1ALA     H2    3   2.853-36893488147419103000.000  -3.040
      .                            .
      .                            .

You can see that there is a large negative number in the middle and this
number remains constant for all atoms, while the first and last real numbers
with three decimals change. Is this the correct form of the out.gro file
to be submitted to grompp (-c out.gro) for a further energy minimization? When 
I did so, the energy minimization was not finished within a half hour on an
SGI workstation using steepest descent and 1000 step at maximum. Formerly, the
procedure lasted for some minutes even with 3600 water molecules in the system

When the editconf is running, I see on the screen:

new system size :  2.160  0.000  2.215
new center      :  2.876-36893485948395848000.000 -2.617 (nm)

The box vectors, angles, and volume reamins unchaged, as expected.

The second value for the new system size is 0. Is it normal? 

Thanks, Peter Nagy
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