On Tue, Oct 22, 2019, Andrea H. Kasun wrote:
>
>I have a problem with MD simulations of a small enzyme with its substrate.
>When I use iwrap=1 option....
Glad that autoimage worked. But I'll just note that using iwrap=1
should almost never be needed anymore, and you might just consider
leaving it at its default value of 0.
Explanation: imaging a trajectory to get what you "want" is a tough
task: Dan has put a lot of smarts into autoimage in cpptraj, but even
with that, there are still a number of options that may be needed.
The iwrap=1 code to do this on-the-fly is the simplest (dumbest) variant
of this, and will often not do the "right thing". I've pressed to
eliminate this option, but there are few (rare) cases where using it may
be the best option. But as long as you are using netcdf restart files
(the default for several years now), be sure you really need/want
iwrap=1 before setting it.
...thx..dac
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Received on Tue Oct 22 2019 - 06:00:02 PDT
