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

From: Aron Broom (broomsday_at_gmail.com)
Date: Sun May 13 2012 - 09:16:26 CDT

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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