[gmx-users] Pull code/starting structures
burisch at bph.ruhr-uni-bochum.de
Tue Nov 20 18:08:42 CET 2001
for my diploma thesis I have to simulate a protein with a small buried
ligand. I want to force the ligand to diffuse out of the protein,
taking a yet unknown path. Then I want to do some free energy
calculation with the mean force necessary for pushing/pulling the
At first glance the starting structure pull code of Gromacs 3.0.5
seems to be the way to go (any other suggestions?), but I'm a little
bit confused about the whole algorithm in general and the parameters
in the .ppa input file in particular:
What exactly is the use of "r0_group2" and what shall I do with the
generated out_<something>.gro structures, which are created in the
given distance of the reference structure?
I managed as a test to pull in vacuo one of the ligand molecules from
a distance of 2 nm to a (freezed) other one, but trying to push the
molecules away from another (with the reference ligand freezed again)
doesn't work, i. e. the parameter "reverse" seems always to be set to
In all cases I set the "r0_group2" to 0.0 0.0 0.0 (no
out_<something>.gro stuff was created then ;-)) and the "transstep"
and "tolerance" to zero.
And finally where do I get the force for pulling from (the .pdo file
seems to contain only coordinates)?
Any hints are much appreciated!
Thanks in advance for your help, Christian
PS: The freezing of the reference structure isn't the cause of my
"from_reference" problem, I just tried it without.
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