Dear GROMACS users,
I used the new Pull Geometry angle-axis to define the angle between a
peptide (with two c-alpha atoms) and the z-axis as pull coordinate. I have
generated a pull trajectory where
this angle changes over time from about 80 degree to 0 degree
approximately, over the
total time
Dear GROMACS user,
I use the pull code to pull one peptide away from a larger globular
protein. For subsequent Umbrella Sampling analyses, I want to keep the
peptide within a certain (cylindric, say) volume.
However, I want to define the longitudinal axis of the cylider running
parallel to the
frames from pull.xtc and I do not see each COM-COM distance
that would be required to have exactly, say, 0.1 nm
spacing, so I use a script which selects frames which resemble 0.1 nm
spacing as closely as possible, so there might some deviation.
2016-06-16 21:24 GMT+02:00 Lukas Zimmermann <luk
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Lukas
> Zimmermann <luk.zi...@gmail.com>
> Sent: 15 June 2016 12:45:51
> To: gmx-us...@gromacs.org
> Subject
Dear GROMACS community,
I performed umbrella sampling study to estimate the binding free energy
between a globular
protein with 568 residues and a small peptide with 13 residues. I use the
pull code with k = 800 and rate = 0.005 to generate the initial
conformations over the time course of 1200
Dear GROMACS users,
I am interested in the role of the mdp parameter pull-coord?-dim when
sampling
a particular umbrella window after having generated initial configurations
for, say, the
COM distance between two groups being the reaction coordinate.
I know that these options can be controlled
