[gmx-users] Placing a peptide at the air/water interface

Mark Abraham Mark.Abraham at anu.edu.au
Sun Nov 4 13:01:40 CET 2007

> 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.


More information about the gromacs.org_gmx-users mailing list