the molecule rotates during the MD run

From: Soonmin Jang <>
Date: Mon 3 Dec 2001 23:46:42 -0900 (GMT+9)

Dear Amberers,
I am running small peptides MD with Generalized Born potential.
The problem is that the whole peptide (about 20 residues) is
begin to rotate after couple of nano seconds. The resulting
peptide shape after this time is linear due to the centifuge force of the
rotating peptide(I think).
I used non-rotating and non-translational options. Still the
molecule (peptide) rotates during the MD run !
Is this because AMBER can not completely zero out the rotating
constraint (numerically) so that the rotation happens inevitably
after long time MD run( say couple of nano seconds) ?

Any idea or suggestions ?
Thank you.

Received on Tue Dec 04 2001 - 00:46:42 PST
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