Dear Amber Users!
This time I'm in charge with running of several identical systems consisted
of membrane receptor within the membrane (the difference actually only in
the ligands within the cavity of the receptor). For those simulations I'm
using my equilibration protocol consisted of the NVT 2-step heating with
position restrains applied on the receptor's atoms, and further 2 steps of
the NPT equilibration w/o of any restrains. After this I run production run
which I use for the MMGBSA analysis. From this (md run) typically first
15-20ns is considered as the equilibration and the last 50-70 is used for
the mmgbsa. Approximately in 2 of the 10 simulations of the identical
systems I got crash during those first 15-20ns period with the skinnb error
which associated with the rapid alterations in the box dimensions during
the lipids equilibration around the receptor. Typically I modify this term
only during last stage in NPT equilibration phase but not in the beginning
of the stage where actually I got the crash
#npt
&ewald
skinnb=5, ! Increase skinnb to avoid skinnb errors
After this if I run new simulation from the last checkpoint where I got the
crash- all go fine.
So the question whether I should to modify this term also during beginning
of the production run (e.g use skinnb=3) to avoid the crash or there are
any other solutions here?
Thanks for help,
James
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Received on Tue Feb 10 2015 - 08:00:02 PST
