I checked the *.trr, it does in fact show the coordinates in
double-precision (as opposed to the output *.tpr file). I don't know
why this is, but as long as I get a decent enough max. fore (i.e.
~1E-05) I'll just leave it at that. I didn't see anything relevant in
the *.edr file, so I'll just include the *.trr every time I run NMA.
The em step is not specified in the nm.mdp file, so I guess I could
add it (and specify 1E-05) and I hope that will help.
Thanks again.
Inon.
Quoting "Ran Friedman" <[EMAIL PROTECTED]>:
Inon Sharony wrote:
so it's an improvement of more than 6 orders of magnitude! Could
it be
that the *.trr file have the coordinates in double-precision?
Right.
Not to be petty, but still, I had a max. force of
5.38105464411935e-05
using the minimization procedure, and the Hessian calculation only
got
4.32762e-04. That's still an order of magnitude that does not
transfer
from the energy minimization step to the Hessian calculation step.
Why?
Sounds strange. You can try to save the forces in the trr and see
if it
gets more accurate. Also, do you use the same emstep as in the em
file?
I guess this determines the displacement in NMA as well.
Ran.
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