From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Tue Jul 12 2011 - 15:08:51 CDT
Dear NAMD users,
I ran into the "Low global exclusion count errors" after about 20 ns of production dynamics.
1). I increased the pairlist distance and set "COMmotion no" after the first instance, but still encountered the same error around ~20-23 ns. Temperature, potential and kinetic energies are all stable throughout.
2). After reading the section on "Bad global exclusion count errors" on this link: http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting
I included the "splitPatch position" option set "rigidbonds none" and "COMmotion no." Now the temperature is no longer maintained at 310K, adopting values between 300 and 700 K, and as high as 1300 K. I recently saw Axel Kohlmeyer's post (Re: namd-l: temperature-TS with NAMDplot) suggesting that the lack of rigidbonds may result in poor conservation of energy.
Any suggestions will be appreciated.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:27 CST