[gmx-users] Placing a peptide at the air/water interface
Mark.Abraham at anu.edu.au
Sun Nov 4 13:01:40 CET 2007
OZGE ENGIN wrote:
> Hi all,
> I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface.
> I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values.
editconf -c doesn't place a solute in a box...
> How can I place the peptide at air/water interface before starting a simulation?
I think you want to construct your solvent box as above, then use genbox
-cp solute.gro -cs twophases.gro with an appopriate -box setting.
Alternatively, set up your peptide with its hydrophobic face parallel to
the x-y plane, solvate in a box of water and then delete all waters with
z coordinates past a certain value. Then solvate the water+peptide in
a cunningly chosen box of air.
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