[gmx-users] Re: Hi

[Anton Feenstra]

Dinesh Pinisetty wrote:
> 
> 
> 
> Hi Dr.Anton,
>         I have question to ask you.
> I have a pdb file with DPPC molecule,I created a bilayer from it using
> genconf and editconf.Then i intended to add water molecules through
> genbox.Intially I had 96 molecules in the topology file but after
> performing addition of water through genbox command the topology was
> changed and it shows that the SOl molecules added are 64,245.This value
> looked weird to me.i want to have only 60 molecules per lipid so
> (96*60)5760 water molecules.
>   How can you add only these many molecules using genbox,does genbox by
> default add these many water molecules everytime I use it.

Genbox by default will fill the box specified in the input file (or from
the commandline) with water, and removes all water that overlaps with your
(solute) molecules, e.g. lipids or protein. So the size of your box
determines the number of water molecules added.


P.S., it is most convenient if you ask these questions through the Gromacs
mailing list (I've sent this reply there also).

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Room P275  Tel: +31 20 44 47608  Fax: +31 20 44 47610 |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "It is Lunchtime" (A.R. Van Buuren)                   |
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