[gmx-users] why no. of atoms doesn't match?

Albert mailmd2011 at gmail.com
Mon Apr 15 20:03:17 CEST 2013

Hello Justin and bv08ay:

   thanks a lot for kind reply. I count each component by isolating them 
one by one:

1. protein generated by pdb2gmx command: 4739 atoms in all
2. ligand: 79 atoms
3. chelostrol: 74x42= 3108 atoms
4. popc: 116x96= 11368 atoms
5. solvent: 10079x3= 30237 atoms

total: 49531

all the above results I double check the no. of coponent and total line 
(which represent the atom no.) with gedit, the total atoms is 49621. The 
toplogy give correct no. of each component, and the total no. of such 
component should be 49621 instead of what claimed by Gromacs " does not 
match topology (topol.top, 51295) "

It is correct with the topology I defined at the end of topol.top file:

[ molecules ]
; Compound        #mols
Protein     1
LIG    1
CHL1    42
POPC    98
SOL    10079

thank you very much

On 04/15/2013 07:45 PM, Justin Lemkul wrote:
> Seriously though, the answer to this question is always the same.  
> You're not counting something right.  The solution is something only 
> you can determine. Applying grep -c is your friend here.  You're off 
> by 1764 atoms, which may be useful information if any of your 
> molecules are evenly divisible into 1764. Water is, but perhaps other 
> molecules are, as well, depending on their representation.
> -Justin 

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