[AMBER] strip :WAT command in ptraj

From: Daniel Scott <dscott5.nd.edu>
Date: Tue, 11 Jan 2011 15:39:52 -0500

Hi Amber users,
The strip :WAT command in a ptraj job script gets rid of the waters,
correct? And if you save this job as: "ptrajout A6WTnoWAT.mdcrd nobox",
e.g., can I then use the "A6WTnoWAT.mdcrd file in the job script to
calculate time correlation functions and other ptraj commands at a much
faster rate since the waters are gone? See the following job script as an
example:

trajin A6WTnoWAT2.mdcrd
vector D26CO .365 corr @366
analyze timecorr vec1 D26CO tstep 200 tcorr 20000000.0 out
D26COcorrnoWAT.out

Thanks,
Daniel Scott
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Received on Tue Jan 11 2011 - 13:00:04 PST
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