[gmx-users] Pull code/starting structures

Christian Burisch burisch at bph.ruhr-uni-bochum.de
Tue Nov 20 18:08:42 CET 2001

Hi everyone,

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 
ligand out.
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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