From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun May 13 2012 - 08:23:53 CDT
I grepped the source code and found it has to do with GBIS (specifically in
Molecule.C)
if ( (atoms[i].mass<1.5) != (lcpoParamType[i]==0) ) {
CkPrintf("ERROR\n");
So apparently you have some atoms that aren't hydrogen (lcpo type of 0) but
have a mass of less than 1.5?
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of ypg
Sent: Sunday, May 13, 2012 2:15 AM
To: namd-l
Subject: namd-l: five 'ERROR' in the log file of NAMD2.9
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
ERROR
ERROR
ERROR
ERROR
ERROR
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!
ypg
_____
2012-05-13
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