Re: [AMBER] Particles diffuse very far away from each other

From: Jason Swails <>
Date: Tue, 28 Aug 2012 02:12:40 -0400

On Tue, Aug 28, 2012 at 1:11 AM, ariana karakutuk <> wrote:

> Hello all,
> I'm new in AMBER and trying to learn more,I'm simulating an linear protein
> (120 residues) and I have 3 ions. I'm using GB method.

Do not use explicit ions with GB. Use the 'saltcon' variable to add an
ionic strength/salt concentration to your simulation.

> I've done minimizing and heating (7 stages), but when I've tried to
> equilibrate it has sad:
> I could not understand line
> 901:6835.5128068************-326.2661063************************************
> *s in the inpcrd file often indicate an overflow of the Fortran format
> used to store coordinates in the inpcrd/restart files. This often happens
> when particles diffuse very far away from each other.

This error message is significantly improved from previous versions, and in
fact tells you exactly what happened. If you look at line 901 of your
inpcrd file, you will see all of those stars, which is caused by particles
diffusing very far away from each other. This is because the ions are not
bound anywhere, and simply migrate away from your system.

Also, I had a hard time understanding your email, since all of the carriage
returns were apparently deleted. If that is fixed, it will make it easier
for others to help. (Or am I the only one with this problem?)


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Aug 27 2012 - 23:30:04 PDT
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