Hi AMBER users,
If I have a gzipped trajectory file, the following ptraj command writes a
new trajectory file (.mdcrd) without the water:
trajin A6WT_0_md_prod_1.mdcrd.gz
strip :WAT
trajout A6WTnoWAT.mdcrd nobox
Can I then calculate other ptraj commands (i.e., "dihedral," "analyze
timecorr," etc.) using these commands:
trajin A6WTnoWAT.mdcrd
vector D26CO .365 corr .366
analyze timecorr vec1 D26CO tstep 200 tcorr 20000000.0 out D26COcorr.out
so that the time correlation function calculations are a lot faster? You
see, I have 100 of these .gz files, and it takes about 24hrs for a ptraj
calculation to run. I'm trying to save time by writing a new trajectory
file without the waters.
Thanks for any advice,
Daniel Scott
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Received on Mon Jan 10 2011 - 15:00:03 PST
