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 - 08:00:04 PDT
