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

From: Aust, Susanne <>
Date: Wed, 8 Jul 2009 07:47:56 +0100

Dear Hlengisizwe,
so I understand the steered MD calculation, you can modify only one distance.
But there is a new tool in Amber 11, which you can also use with Amber10,
which called LCOD method.
please look in the tutorial A10, there you can find the script and more
Best wishes!

-----Ursprüngliche Nachricht-----
Von: []Im
Auftrag von Hlengisizwe Ndlovu
Gesendet: 07 July 2009 15:28
Betreff: [AMBER] Steered MD---more than one pair of atoms


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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