Dear Dr. Gandhi,
I guess.. your system has anomalous contacts between
Phosphate and ions, thus causing huge vdW interaction energy.
If you already tried minimization and the problem was not improved..
How about setting smaller dt and tempt, e.g. dt=0.0001 and tempt = 0.1,
Until the system energy is stabilized.
They might help to avoid energy divergence.
Ikuo KURISAKI
-----Original Message-----
From: Neha Gandhi [mailto:n.gandhiau.gmail.com]
Sent: Monday, March 18, 2013 11:04 PM
To: AMBER Mailing List
Subject: [AMBER] ions (salt concentration) and deep energetics problem
Dear List,
I ran a system with phosphorylated residue using amber ff10 force field and
tip3p water potential (presence of counterions). I am trying to run the
same system but with a salt concentration of 0.05 M which adds upt 4 Na+
and 4 Cl- ions in addition to the counterions however, the system keeps
blowing up. It encounters deep energetics problems or vlimit exceeded.
Since it didn't happened to the original system in absence of NaCl, I
speculated that the problem might arise because of electrostatics of Na+
and Cl- ions. I checked the mailing list and I followed the same steps as
mentioned in the list (
http://archive.ambermd.org/201207/0059.html) after
solvating the box. I tried adding ions one by one rather than together at
same time but still the system keeps blowing up after minimization. I am
using ntt=1.
Your help is appreciated.
Thank you in advance,
--
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
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Received on Mon Mar 18 2013 - 18:00:02 PDT
