Hi all,
I have performed a remd with a 250.000 number of exchange trials during the
simulation every 0.5 ps. I have set ntwx=5.000 so I would expect 25.000
structures in my simulation but after processing the data using the script
to extract the coordinates at different temperatures I get
#!/bin/csh
ptraj l_dermorphin.prmtop << EOF
trajin remd.mdcrd.001 remdtraj remdtrajtemp 300.0
trajout remd.300K.mdcrd nobox
distance d1 out dist.300K.dat :1.CA :7.CA
go
EOF
which reads all the output files
Processing AMBER REMD trajectory (new format) files remd.mdcrd.001 ->
remd.mdcrd.010
I only get 19999 structures - when I grep *REMD*' in the mdcrd.001 file I
get 25.000 lines with REMD as expected. I do not know where my mistake is
any help appreciated
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Received on Mon Sep 13 2010 - 03:30:03 PDT
