Hello GROMACS users!
I've posted a few questions in the last few days about
double-precision energy minimization for normal mode analysis, and
everything seems OK except I've been having a re-occurring problem:
The energy minimization procedure ends in
Amazing! It didn't say anything about double-precision, and I got:
Maximum force: 4.32762e-04
(this is from the Hessian calculation, after minimization that got
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax 1e-06
writing
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
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
Inon Sharony wrote:
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
This means that although the minimization was run in double precision,
the atomic configuration is saved in single precision (the last two
decimal places are not used). Does this mean that each time the
optimized *.gro file is re-read, it needs to optimize these last two
decimal
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