[gmx-users] Re: Ligand-protein interaction scoring

[Michael Brunsteiner]

--- Douglas Houston <douglas at davapc1.bioch.dundee.ac.uk> wrote:
> Hi,
> 
> > If you talk about changes somewhere in the range of 0.001 Angstrom
> or
> > smaller this is normal and due to the finite precision/rounding
> errors
> > ...should not worry you.
> 
> An example from the mdrun input .gro file:
>     1THR    OG1    7   2.906   6.619  11.326
> 
> An example from the mdrun output .gro file:
>     1THR    OG1    7   2.898   6.621  11.325
> 
> The largest coordinate shift here is 0.008 of a nm, rather than 0.001
> of
> an Angstrom.

when i set nsteps=0 then I get occasionaly a difference
of 0.001 [nm] between some coords in conf.gro and confout.gro
no matter what system
... what you got there looks like it was more than a 
rounding error ...

> Is there some EM/MD going on here that I haven't
> switched
> off?

what's in your md.mdp file ?

> 
> Thanks,
> 
> Doug
> 
> 
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