Qin Qiao wrote:
Dear all,
I came across a problem when I want to make the REMD trajectories
continuous.
What I did:
1. 'demux.pl <http://demux.pl> REMD_0.log' --to get the
'replica_index.xvg'
2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg'
It seems smooth. But when I check the rmsd of the output 0_resort.xtc, I
found it's still discontinuous.. with big jumps about 0.5nm..! Could you
help me to figure out what's wrong? Thanks a lot.
Have you properly accounted for periodicity effects?
-Justin
Best,
Qin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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