Hi all,
I want to update my own post for any user that could have similar issues in the
future. The issue that I described before (large spikes were observed in the
values reported in pullx file but when i calculated the same restrained
distance using “gmx distance” no such spikes were observed)
Hi Mark,
Thanks for your comment. No, that is not the problem. At that location
the center of mass of the peptide is deep inside the membrane,
separation between the two pulling groups is 0.4 nm and the dimension of
the cell along z is more than 10 nm. I am only pulling along the z
direction.
Hi,
My (thoroughly uneducated) guess is that the spikes are related to the pull
distance approaching half of the dimensions of the cell. Not all flavours
of pulling can handle this. Might that be the issue?
Mark
On Sat, Feb 24, 2018, 17:55 alfredo wrote:
> Hi,
> Updating my post. The problem
Hi,
Updating my post. The problem has been observed in two different machine
systems (the latest I have found the problem was the skylake nodes in
tacc). I assumed it has to be some communication bug of coordinates and
forces in the pull part of the code. Probably observed in my case
because o
Hi,
I am using gromacs to get the PMF of a peptide of about 20 amino acids, moving
inside of a bilayer membrane. After pulling the peptide inside the membrane now
I am using pull-coord1-type = umbrella
and pull-coord1-geometry = distance to sample configurations in each window
for the umbrell
