From: ypg (ypg_at_biophy.nju.edu.cn)
Date: Sun May 13 2012 - 09:48:18 CDT
Actually, I haven't used GB model.
Maybe it's just a safety check for GBIS calcultion and that is why it didn't terminate my simulation.
2012-05-13
ypg
发件人： Aron Broom
发送时间： 2012-05-13 22:13:46
收件人： ypg
抄送： JC Gumbart; namd-l
主题： Re: namd-l: five 'ERROR' in the log file of NAMD2.9
but for your new hydrogen types, are you sure LCPO will handle them properly for the SASA part of the GBIS calculation?
On Sun, May 13, 2012 at 10:13 AM, ypg <ypg_at_biophy.nju.edu.cn> wrote:
Oh, I think that is the point, because I have defined five new type 'H' atoms in my parameter file for convenience.
Thank you so much for your help!!
BTW, would such atoms cause any problems in simulation? Since my timestep is 2fs, I think they should be constrained like other hydrogen atoms in principle.
2012-05-13
ypg
发件人： JC Gumbart
发送时间： 2012-05-13 21:23:48
收件人： 'ypg'; 'namd-l'
抄送：
主题： RE: namd-l: five 'ERROR' in the log file of NAMD2.9
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
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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