On Mon, Aug 17, 2015, Chinh Su Tran To wrote:
>
> I run minimization and ALPB (implicit) for my system, and I got ***** in my
> results. However, the process is still running without any termination.
>
> Taking a look at the result out file, I found the energy values very high
> and making no sense. But I was wondering why it still goes on!
>
> May I know what causes those signs? Isn't it caused by the clashes in the
> structures or the structure was not properly minimized? (I did manually
> added some residues at the C-terminus using PyMOL before running LEAP)
Looks like you need to do more minimization, perhaps. Also, use the same
parameters in minimization as in MD. Then run MD in shorter increments, and
save a restart shortly before you see bad behavior. Start from the last good
restart and use much shorter values of nstlim and ntpr. Visualize the
trajectory to see if you can what is going on.
Also, try a standard GB run on the same system. The alpb option is very
rarely used, and it is possible that the problem arises from that source;
comparing to a standard run will help narrow things down.
The "***" when a number is too large to fit into a given format (number of
characters) in the output file.
...good luck....dac
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Received on Mon Aug 17 2015 - 05:00:05 PDT
