[AMBER] How to do analysis on specific frames in cpptraj?

From: XP Chen via AMBER <amber.ambermd.org>
Date: Tue, 21 Feb 2023 20:02:45 +0800 (CST)

I want to do some analysis (here is `watershell`) on some specific frames.

I use a not-easy way as follows. However, it will create new trajectory files, and make it not convenient for large trajectories. Is there any elegant way to do analysis on specific frames which do not fulfill `<start> <stop> <offset>` in `trajin`?

1. First split the trajectory
parm A.prmtop
trajin A.nc

trajout B1.nc netcdf onlyframes 1,78,100,101,170
trajout B2.nc netcdf onlyframes 8,82,88,99,120,125

2. Then reload the new trajectory and do the analysis
parm A.prmtop
trajin B1.nc

watershell :5.SG out wa.out lower 3.5 upper 5.0 :WAT

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Received on Tue Feb 21 2023 - 04:30:03 PST
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