Subject: help about charmm

From: wei <[email-masked]>
Date: Tue, 5 Nov 2002 15:00:30 +0000

Hi, all:

I want to use charmm to  minimize a big protein system(about 6600 atoms 
without exclude solvent). and in the output file, it said the following 
things about Nonbond properties. I am worrying about the statement "Maximum 
group spatial extent (12A) exceeded.Size is  15.85 Angstroms and starts with 
atom:    6046".

Is this serious? Do I have to do something or just let it be? 

Wei Zhuang

*****************************************************************************************
CHARMM>    NBONDS CUTNb 100.0 CTOFnb 99.0 CTONnb 98.0

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    CDIElec  SHIFt    VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  =100.000 CTEXNB =999.000 CTONNB = 98.000 CTOFNB = 99.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  1.000 EPS    =  1.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found  19029 exclusions and  17626 interactions(1-4)
 <MAKGRP> found   5397 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 VEHEAP> Expanding heap size by21954560 words.
 == PRIMARY == SPACE FOR 21826225 ATOM PAIRS AND        0 GROUP PAIRS
 NBONDA>>  Maximum group spatial extent (12A) exceeded.
   Size is       15.85 Angstroms and starts with atom:    6046
   Please check group boundary definitions.
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