hi
No, they are not the softcore parts. They are a CH group on the pyridine
ring I'm modifying. And I'm checking the atom/bond order. They seem
consistent.
Victor
On Wed, Aug 3, 2011 at 9:58 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > Checking for mismatched coordinates.
> > Molecule 1 is partially softcore on this side or the
> > corresponding
> > partner molecule is.
> > Checking for SHAKE constraints on bonds crossing into the SC region
>
> this is not really a warning, it just tells you what sander is doing at
> this point and if it makes any adjustment/finds any problems (none in your
> case)
>
> > A large portion of the lamda runs went through successfully and the
> > results
> > looks reasonable. However I do have failed calculations as well. This is
> > the
> > error message:
> > vlimit exceeded for step 19883; vmax = 25.4647
> > vlimit exceeded for step 19884; vmax = 3280.2326
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 3 1 58 64
>
> Are atoms I and J (58&64) in your soft core region?
>
> It is hard to diagnose this without knowing what your trajectory looks
> like, but such problems can be caused by the non-softcore parts
> coordinates drifting apart on both processes. Normally, sander should
> prevent this, but I have seen problems caused by different atom/bond
> orders in the prmtop files. If you can narrow this down to a single test
> case that reproducibly fails without having to run 100k steps, you can
> send the test case to me (not the whole list) and I'll check if I see
> something problematic.
>
> Kind Regards,
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Wed Aug 03 2011 - 08:30:03 PDT
