Hi,
I am running REMD and use ptraj to extract trajectories from mdcrd outputs.
I first concatenate all replica trajectories files:
Here is the scritpt
#!/bin/bash
for R in 001 002 003 004 005 006 007 008 009 010 011 012 013 014 015 016 017 018 019 020 021 022 023 024 025 026 027 028 029 030 031 032 033 034 035 036 037 038 039 040 041 042 043 044 045 046 047 048 049 050 051 052 053 054 055 056 057 058 059 060 061 062 063 064 065 066 067 068 069 070 071 072 073 074 075 076 077 078 079 080;
do
cat remd.mdcrd.$R remd_r2.mdcrd.$R remd_r3.mdcrd.$R remd_r4.mdcrd.$R remd_r5.mdcrd.$R remd_r6.mdcrd.$R remd_r7.mdcrd.$R remd_r8.mdcrd.$R remd_r9.mdcrd.$R remd_r10.mdcrd.$R remd_r11.mdcrd.$R remd_r12.mdcrd.$R remd_r13.mdcrd.$R remd_r14.mdcrd.$R remd_r15.mdcrd.$R remd_r16.mdcrd.$R remd_r17.mdcrd.$R remd_r18.mdcrd.$R remd_r19.mdcrd.$R> Remd.mdcrd.$R
done
And then extract the temperature trajectories.
Here is the script
#!/bin/bash
ptraj AVP_open.prmtop <<EOF
trajin Remd.mdcrd.001 remdtraj remdtrajtemp 302.28
trajout remd_302K.mdcrd nobox
go
EOF
When I run the second script I get this error:
Done.
1% ..
REMDTRAJ: Final repTemp value read= 369.920000, set 590
Could not find target 302.280000 in any of the replica trajectories.
Check that all replica trajectory files were found and that
none of the trajectories are corrupted (e.g. missing a temperature).
ptrajProcessInputCoordinates(): Target replica temperature not found in traj! 100%
PTRAJ: Successfully read in 589 sets and processed 589 sets.
Dumping accumulated results (if any)
Does any one know why?
Thanks a lot,
Nawel
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Received on Fri Jul 04 2014 - 06:30:02 PDT
