[gmx-users] peptide into surface

Alexander Alexander alexanderwien2k at gmail.com
Sat May 7 23:29:52 CEST 2016

Dear gromacs user,

My task is to study the adsorption of a solvated short peptide onto a solid
surface using gromcas in periodic boundary condition. So, the system
contains a solid surface as "substrate" and "water+peptide" on top.

To do so, I follow the procedures or sequence as below, would you please
let me know if the procedures and sequence are right? any comment is highly

Best regards,

1.First equilibrating the "surface" and "peptide+water" separately as below:

 1.1 Energy minimization + NVT equilibration for surface.

 1.2 Exactly like the Lysozyme in water tutorial, an energy minimization +
NVT equilibration + NPT equilibration for the solvated peptide in a box as
big as the the vacuum box in top of the surface in the last step.

2. And then merging the two equilibrated system together and then again
doing an energy minimization + NVT equilibration for the whole system
before the final MD production.

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