From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Tue Oct 09 2012 - 08:48:43 CDT
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.
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
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