[gmx-users] Specifying the number of waters

Chris Neale chris.neale at utoronto.ca
Tue Dec 4 23:26:01 CET 2007

> I would like to set up two peptide simulations (with different peptide
> conformations) that have the same number of water molecules in truncated
> octahedral boxes with periodic boundary conditions.  Can anyone suggest a
> good way to specify that the same number of waters be added for each of
> these two simulations?

I can think of 3 options:

1. get your two systems close to the same number by iterating through 
editconf -d N; genbox; until you find an N that leads to approximately 
the same number of waters. Then just remove some randomly selected 
waters. equilibrate using position restraints on your peptide and 
constant pressure.

2. As an alternative idea, create system A, then create system B by 
simply pasting the waters from system A together with the peptide from B 
(yes they will crash but don't worry). Then, once system A is 
equilibrated, apply position restraints using -r systemB.gro so that 
system A will migrate to the system B conformation.

3. Consider that you don't need to do this. I once thought that I did 
but it was actually lots more trouble than it's worth.


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