On Mon, Mar 18, 2013, Neha Gandhi wrote:
>
> I ran a system with phosphorylated residue using amber ff10 force field and
> tip3p water potential (presence of counterions). I am trying to run the
> same system but with a salt concentration of 0.05 M which adds upt 4 Na+
> and 4 Cl- ions in addition to the counterions however, the system keeps
> blowing up.
You'll have to mostly debug this yourself, since only you know exactly what
you did. Check first to see if the problem is unique to the way in which you
created the phosphorylated residue (i.e.: do you still have problems with a
standard amino acid?)
Then, stop the simulation as close as you can before the problems appear, and
look at the coordinates of the system. Try to identify the what bad
interactions (e.g. close contacts) are leading to the behavior you see.
...good luck...dac
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Received on Tue Mar 19 2013 - 05:30:04 PDT
