Re: [AMBER] vlimit exceeded for step

From: David A Case <>
Date: Mon, 5 Mar 2018 08:09:28 -0500

On Thu, Mar 01, 2018, ASMITA SEN wrote:
> vlimit exceeded for step 5804; vmax = 32.7330
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 2333 4822 4823
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.

As the message says, there is probably something wrong with the
simulation or force field. As a start, look at the region around atoms
4822 and 4823. Are these part of standard residues, or part of
something else, like the iron-containing moiety? See if you can look at
a restart file as close as possible to the time the SHAKE failure
happened, and look for problems (like very short non-bonded overlaps).
[The "checkoverlap" action in cpptraj can be very helpful here.]

Also, check the van der Waals radius of the hydrogen in the Fe-OH group:
if it is zero, that might lead to the sorts of problems you are seeing.
Of course, the problem might be somewhere else entirely.

...good luck...dac

AMBER mailing list
Received on Mon Mar 05 2018 - 05:30:03 PST
Custom Search