Re: [AMBER] Error while umbrella sampling with distance restraint

From: Jason Swails <>
Date: Fri, 26 Jul 2013 15:13:00 -0400

On Fri, Jul 26, 2013 at 12:36 PM, Meekyum Olivia Kim <>wrote:

> Hi,
> Thank both of you for your replies. But I couldn't visualize the system
> after the minimization since the minimization restart file has values of
> *********** in those lines where the errors occurred.

Then visualize the structure before. This, along with the minimization
output file, should contain enough clues for you to at least narrow down
the problem.

The *****s in the restart file basically mean one of the coordinates is
getting very, very large -- i.e., one of the coordinates of one of the
atoms is over 1000 away from the center of mass of the whole system in
one direction. That is a huge distance, and very likely indicates
something very weird (and wrong) with your initial system structure. You
have to find this.

Try and hypothesize a reason, based on your observations of the output file
and initial structure, that you believe explains your errors. Then, try
and come up with an approach to solve the problem you hypothesized. (As a
hint, the problem always appears simple in hindsight).

Do you think a longer
> minimization can solve this?

No. If the first steps of a minimization is blowing a system apart,
there's no reason to believe that allowing it to run longer will bring
everything back together.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jul 26 2013 - 12:30:03 PDT
Custom Search