AMBER Archive (2009)

Subject: [AMBER] Steered MD---more than one pair of atoms

From: Hlengisizwe Ndlovu (
Date: Tue Jul 07 2009 - 08:27:59 CDT


I have been learning how to carry out SMD on amber 10. I have had
success in a number of 'toy' simulations where i increase the distance
between two atoms as set out in the manual. I now want to specify
three pairs of atoms for which i wish to increase the distance of
separation. Howere, all my attempts at specifying these in the
dist.RST file have so far proved unsuccessful.

Any pointers on how to specify more than one pair of 'SMD-atoms' at a
time in the dist.RST file??


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