Hi Tsjerk,
Thanks for the advice.
After I did the nojump conversion of trajectories, there were still quite a
few frames with min. dist. under 2.0 nm, but all of them were above 1.4 nm,
which I set for rvdw.
This is not ideal, but I wonder if it's still OK to use this trajectory?
Thanks,
Yun
Hi Yun,
Well, within 2 nm periodic images can influence each other through ordering
of water. But how much that will affect your results and how relevant it is
for the properties you're after is hard to tell. I think most people will
just continue with analysis, saying that there have been no
Sorry, I just found that even if I use a dodecahedron box with -d 1.2 nm,
the min periodic image dist still dropped abruptly to 0.172 or something
like this after around 35 ns or 30 ns (different trajectory with same
topology).
So I wonder if this is just inevitable and we should live with it?
Hi Yun,
Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before
using g_mindist.
Also visually check a frame that is reported to have closed contacts.
Hope it helps,
Tsjerk
On Nov 10, 2011 1:45 AM, Yun Shi yunsh...@gmail.com wrote:
Sorry, I just found that even if I use a
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