AMBER: cut-off & MD

From: <>
Date: Mon, 06 Dec 2004 13:49:04 PDT

Hello, Amber:

I have a question related to ‘cutoff’ for MD simulation. I have ~3 ns run
with my protein model. When I check the distance of one pair of
salt-bridge & time, the distances (E103.OE2-R122.NH1) remains under 3.5A
at most of time, but jump up to 5.2A at certain time period (last about
0.4 ns). When I exam the trajotoies from this time period, the two
residues still form H-bonds at E103.OE1-R122.NH1. When I repeat the run
with the model including the target mutants, there is no distance
jumping up (E103.OE2-R122.NH1) and staying about 2.7-3.6A., indicating a
stabilized effect from these mutants.

I didn’t set up the specific cut-off for the MD runs. So all the runs
have a default cutoff setting at 8A. With my wide-type protein model,
there are only significant conformation changes on that particular
‘salt-bridge’, but not breaking the H-bond. I am not sure if the cut-off
values have some kinds of effect on it. I plan to try some replica runs
with different cut-off values, to see if the links between the two
residues break or not. Could you give me some comments if this is the
reasonable way? Do the simulation time will be increased a lot with
cut-off = 20 compared with cut-off =8?

I use Amber7 and periodic simulation condition.

Thank you for your advices.


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Received on Mon Dec 06 2004 - 21:53:00 PST
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