[gmx-users] Regarding g_rms

[nikhil damle]

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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