[gmx-users] error message

[Xavier Periole]

Maria Sabaye Moghaddam wrote:

>Hi; 
>
> I am getting an error message as follows:
>
>WARNING 1 [file "1s9z.top", line 39]:
>  System has non-zero total charge: 3.000000e+00
>
>processing coordinates...
>double-checking input for internal consistency...
>ERROR: One of the box vectors is shorter than twice the cut-off length.
>Increase the box size or decrease rcoulomb.
>Velocities were taken from a Maxwell distribution at 300 K
>There was 1 warning
>Fatal error: There was 1 error
>  
>
That is a classical. The error you have is that you use a cutoff on 
interactions
(elec or vdW) that is smaller that half of the box size, which means that a
molecule would see more than one time the same particules: one in the 
central
box and the other in the image box. You do not want that !!!

Solution: increase your box size or decease your cutoff. The first is 
probably
the best solution.

XAvier

-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
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