Hi,
I am simulating a protein system and willing to compute rmsd over entire
trajectory wrt a starting crystal structure. i use g_rms programme for this
purpose starting from 0th frame until last frame of time. But rmsd shows
abnormal spikes between successive time-frames. Height of spikes is as high as
15A in some cases. But when i compute lsq fit rmsd using g_confrms programme,
it gives rmsd comparable to other neighbouring time-frames. As given in the
manual, both g_confrms and g_rms compute rmsd using lsq fitting of conformers.
so why there should be such a vast difference ??
regards,
Nikhil
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