On Tue, Feb 25, 2014 at 12:42 PM, Mele N. <nm10g13.soton.ac.uk> wrote:
try to found a way to check the overlap with "checkoverlap" because it is
> not really explain in the manual.
>
It's actually in the 'ptraj' section of the AmberTools manual -- see pages
285 and 286 of AmberTools13.pdf. You definitely want to get imaged
distances (which is default).
Tom also gave helpful suggestions, but I still suggest investigating the
root cause of the energy/force explosion that ultimately results in SHAKE
failures. The fixes you should try depend on what's really going wrong.
It's also worth noting that people on this list are not necessarily
packmol experts, so your problems introduce an additional degree of freedom
in the debugging process.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 25 2014 - 10:30:03 PST
