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

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Mon Sep 9 17:33:37 CEST 2002

On Mon, 9 Sep 2002 sekirin at iop.kiev.ua wrote:

>      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
> be
> desirabre to have some documented method.
>      Thank you              I.V.Sekirin

after energy minimization, one has two file: {*}.gro and {*}.trr. Before
doing normal mode analysis, one should use:

grompp -v -f em -c {*}.gro -o {*}_em.tpr -p {*}.top -t {*}.trr

if you do not use  -t {*}.trr then the forces computed from  {*}.gro will
be very large.

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