Thanks, yes there were some issues with the structure.
Can you please tell me how can i determine the direction of pulling while
stretching a DNA double helix?
Also, how one can set/achieve a desired pulling velocity e.g. 5m/s in mdin
file for SMD?
Thank you
On Wed, Jul 2, 2014 at 12:40 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Tue, Jul 01, 2014, Asmita Gupta wrote:
> >
> > 1. When i changed the cut value from 10 to 12, i got different error
> > messages e.g
> >
> > with cut=10, sander terminates with error
> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> >
> > with cut=12, it terminates with
> > vlimit exceeded for step 0; vmax = **********
>
> These are not necessarily different errors. It looks like you have a bad
> initial structure (and so are seeing integration errors on step 0). Have
> you minimized your structure? Used the "checkoverlap" command to look for
> bad
> contacts? I rather doubt that your problem has anything really to do with
> the cutoff you choose.
>
> (If you are running in parallel, switch to serial runs for debugging: that
> way
> you won't miss any of the error messages.)
>
> ....dac
>
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Received on Wed Jul 02 2014 - 07:30:05 PDT
