[gmx-users] about editconf

[Anton Feenstra]

Lieven Buts wrote:
> parinald at unsl.edu.ar wrote:
> 
>>              I run editconf to define the right boxsize for my sistem:
>>  editconf -f ${MOL}.gro -o ${MOL} -d 0.5
>> what`s the meaning of "0.5"?, and how I can change the boxsize or water
>>number?. Thank you.
> 
> 
> According to "man editconf" the value of the "-d" option specifies
> the distance between the solute (protein or whatever) and the edge
> of the box. From this the amount of space for solvent molecules
> follows, although it is of course difficult to exactly determine
> the number of molecules that will be added.

editconf just sets the box size, after that it is still 'empty space'.
In addition, editconf has other options to set a specific box size
and shape (check 'editconf -h', or online manual).

genbox can fill the empty space with water, and will tell you the exact
number of water molecules added.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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