RE: five 'ERROR' in the log file of NAMD2.9

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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