Comparative MD

From: FyD <>
Date: Fri, 11 Jul 2003 15:29:02 +0200 (CEST)

Dear All,

Using AMBER7, we built the prmtop and prmcrd files (of a peptide) needed for a
MD run using the 'sequence' command of leap. We did it twice, both on IRIX-SGIs.
The 2 prmtop files are obviously identical but the 2 prmcrd files present some
very small differences (i.e. on the seventh digits after the decimal point).
Using these 2 sets of prmtop and prmcrd files, we ran the same MD-IGB1
protocole. The 2 MD trajectories are totally different (we follow the backbone
RMSD between a reference structure and the MD snapshots).

Are you surprised by this ?

Thank you very much, best regards, Francois
Received on Fri Jul 11 2003 - 14:53:01 PDT
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