[gmx-users] loss of precision in *.gro

sekirin at iop.kiev.ua sekirin at iop.kiev.ua
Mon Sep 9 17:21:15 CEST 2002

     Dear colleagues,
     Could you please explain me, why the others do not feel the
following problem and how it could be treated:
     After optimization of geometry, we easily obtain (e.g., with
emstep=0.001, emtol=1.0) maximal force ~ 4.5e-1 . However,
the coordinates (in nm) are written into the file confout.gro with
the use of format f8.3 . As a result, precision is only ca. 0.01
Angstrom ,
and we have drastic loss of precision. Naturally, at consequent
normal mode analysis the program reports that the maximal force
is ~ 5.1e2, so the results can be inadequate, etc.
     One can easily demonstrate (by considering diatomic molecule
with variable equilibrium interatomic distance) that just the round-up
is the cause of this effect.
     Evidently this effect _can not_ be avoided by the use of double
precision (as far as format f8.3 is a part of specification of *.gro).
Probably one could surgically cut the coordinates from *.trr (or use
user's own additional output) and insert them into *.tpr, but it would
desirabre to have some documented method.
     Thank you              I.V.Sekirin

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