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
LinkedIn
Research Gate
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 18 2013 - 07:30:02 PDT
