[gmx-users] restart

wnoid at hec.utah.edu wnoid at hec.utah.edu
Fri Feb 10 17:58:14 CET 2006

hello again.

thanks again to mr. yang ye for his reply.  however, i tried the test
again on the xeon cluster with "optimize_fft = no" and my problem
persists.  the trr files are unchanged to within 1 part in 1e5 over two
steps when i turn off the optimize fft option.  (to my mind that is
comforting.)  so this not the problem.  regardless of whether the
optimize_fft variable is yes/no, my continuation script does not reproduce
the gro file from a two step simulation.

i do appreciate that this problem might seem stupid, especially to those
who are interested only in sampling phase space.  but i am interested in
this both to make certain that my scripts are correct and because i have
special interest in studying dynamics.  (yes i do appreciate that md
simulations are chaotic and perhaps it is not sensible to try to place
special significance on the propagation of atomistic force fields anyway,
but that is another question.)  i would just like to make certain that i
my protocol is correct.  just getting the gro file right over two steps
seems not unreasonable to me.

thanks again to mr. yang ye for his suggestion.  thanks to all who looked
at this.  any help would be greatly appreciated.


will noid

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