From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Wed Oct 10 2012 - 05:07:54 CDT
Hi all,
I tried to do the same thing with the same parameter file usin namd - V.2.8.
It is working fine in the last version. However if i tried to do with the new version.
It shows me some warning and Error message without any caption.
After grepping through the source code, i figured out it is because of the following.
if ( (atoms[i].mass<1.5) != (lcpoParamType[i]==0) ) {
CkPrintf("ERROR\n");
Apparently, it occurs because of the hydrogen atoms.
I have three different hydrogen types in my parameter file.
Could anyone help me resolve it.
Thanks in advance,
Sincerely,
Narasimhan
> ----------------------------------------
> From: Narasimhan LOGANATHAN <Narasimhan.Loganathan_at_etu.univ-provence.fr>
> Sent: Tue Oct 09 15:48:43 CEST 2012
> To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
> Subject: namd-l: Warning & error
>
>
> Hi all,
> I am trying to study aqueous-mineral interface using NAMD.
> I created the all the required files(.conf,.rtf,.prm,.pdb)
> I tried to perform the simulation. The simulation is running fine.
> However, when i tried to look at the log file, i find serious of warning followed by Error message without any caption to it.
> I couldnot figure out where is the error and to overcome it.
> A small part of the error is as follows
>
> Info: 0 VDW_PAIRS
> Info: 0 NBTHOLE_PAIRS
> Warning: Residue 10 out of order in segment 0, lookup for additional residues in this segment disabled.
> Warning: Residue 9 out of order in segment 0, lookup for additional residues in this segment disabled.
> ERROR
> ERROR
> Info: TIME FOR READING PSF FILE: 0.117436
> Info: TIME FOR READING PDB FILE: 0.037545
>
> Could you help me to sort the error and how to rectify it.
>
> Another question, from the manual i get the keyword "wrapAll" is used to keep the molecules inside the simulation cell.
> I used it, but some part of the molecules are still present outside the cell. What can i do to keep everything with the simulation cell.
>
> Thanks in advance
>
> Sincerely,
> Narasimhan
>
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