On 3/7/15 3:18 PM, xy21hb wrote:
Dear Gmxers,
What I meant is to use the result of "g_select" as index to calculate e.g.
g_hbond,
Since if I simply use "-n" the g_select index, it will give the selected water
in each frame.
But then how I can average them in gromacs automatically?
Each index group from g_select can be used to analyze the matching frame in the
trajectory. So you need to analyze each frame separately, concatenate the
output, and average. If you assemble a text file (.xvg) that g_analyze can
read, that's one way, otherwise scripting something to calculate an average is
trivial.
-Justin
Thanks,
Yao
At 2015-03-07 06:27:49, "Mark Abraham" <[email protected]> wrote:
Yes, it can. I suspect that's even one of the examples in the selection
help.
Mark
On 06/03/2015 3:43 pm, "xy21hb" <[email protected]> wrote:
Dear GMXers,
I wonder if g_select in GMX5.0 can select some distance e.g. 5A of the
solvent e.g. water w.r.t. a protein dynamically,since different numbers of
the solvent in each time frame should be observed.
Thanks,
Yao
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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