Thanks.
I used the "direction-periodic", along with "semiisotropic" with zero
compressibility in Z direction to have also NPT equilibration in each
windows. Below is the final pressure after NPT equilibration with 1 bar
reference, I hope it would be ok?!
Energy Average
On 10/10/16 4:57 AM, Alex wrote:
Thanks for your response.
My question is not in the sampling step as I have already pulled away two
parts and even picked out the configuration of each windows. But my
question is about simulation in each individual windows toward WHAM.
You means in the step
Thanks for your response.
My question is not in the sampling step as I have already pulled away two
parts and even picked out the configuration of each windows. But my
question is about simulation in each individual windows toward WHAM.
You means in the step six of the tutorial no necessarily
On 10/8/16 2:46 PM, Alex wrote:
Dear gromacs user,
In a PMF simulation of a short peptide on solid surface, I am using the
"direction-periodic" as "pull-coord1-geometry" in the Z direction, then as
you know the equilibration of the system in NPT ensemble is not doable for
the individual
Dear gromacs user,
In a PMF simulation of a short peptide on solid surface, I am using the
"direction-periodic" as "pull-coord1-geometry" in the Z direction, then as
you know the equilibration of the system in NPT ensemble is not doable for
the individual windows. So, for each windows of
