Qin Qiao wrote:
2011/1/7 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Qin Qiao wrote:
2011/1/7 Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>>
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> <http://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
It's the same after I remove periodicity by trjconv -pbc mol -ur
compact ...
One iteration of trjconv is not necessarily enough to produce a
properly imaged trajectory. What is going on in the trajectory when
these spikes are occurring?
-Justin
In VMD, it just seems to change to a different conformation...
Then it sounds like something has gone wrong with the demultiplexing. As for
what that is, it's hard to say. Look into the .log file and resulting .xvg file
(from demux.pl) to make sure that the proper exchanges were identified. Then
try to determine from which replica that sudden change arose (i.e., in which of
the original trajectories was that configuration present). Finding it should be
relatively easy; just dump out the frames at that time point from each of the
trajectories to see.
For further troubleshooting, it would also be useful to know your Gromacs
version, in case there is some sort of bug. It is too early to tell, though,
where the problem lies.
-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 <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
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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