[email protected] wrote:
Hello all,
I am doing a cg minimization with Gromacs-4.0.3.
It is compiled on a Linux system with gcc 3.4.6
All frames in the trajectory are identical to the starting configuration,
except for the final one, which is clearly different.
How are you assessing this? External viewing programs don't always show the
necessary level of detail. If you use trjconv -dump to drop out a few select
frames, and diff the resulting .gro files, are they indeed identical, or are
there small differences?
How different is the final structure? Is there a drastic change? Or is it just
that the change relative to the input structure is more obvious?
I get the expected number of frames in the trajectory (.trr),
and the energy saved in the .edr is decreasing.
But apparently the changes in the structure do not reach the trajectory file.
If the energy is changing, then so too should the structure.
-Justin
Any suggestions?
Heiko
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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