From: ypg (ypg_at_biophy.nju.edu.cn)
Date: Sun May 13 2012 - 02:15:27 CDT
Dear NAMD experts,
There are five strange ERROR symbol appear in my log file produced by NAMD2.9 just like this:
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS /gpfsTMP/wangwei/ypg/NAMD/ff/par_all27_prot_lipid_CRO2.txt
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES YFP+_eq3.restart.coor
Info: SUMMARY OF PARAMETERS:
Info: 194 BONDS
Info: 473 ANGLES
Info: 601 DIHEDRAL
Info: 51 IMPROPER
Info: 6 CROSSTERM
Info: 123 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.243933
Info: TIME FOR READING PDB FILE: 0.0932858
These ERRORs would not appear if I use NAMD2.7.
It seems that there is something wrong in my force field file, and I indeed have modified my parameter file to define a new type residue. However, these ERRORs would not terminate my simulations and I can still obtain plausible MD results. Also, ERRORs only appear when my system involve the new type residue.
Now I'm really worrying about the validity of my simulated results. I will be highly appreciate for any help!
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:58 CST