[gmx-users] Pulling code

alicia at biof.ufrj.br alicia at biof.ufrj.br
Fri Nov 8 13:58:08 CET 2002

Hi Frauke,
It's great to know that someone else is working with the pull code; we can join 
our efforts! I sent to Justin, as he requested, the impute files of the system 
I'm working on, as well as the file.ppa (output file). I hope that he had had 
some time to deal with them! I never tried to pull two groups simultaneously, 
so I don't know about that problem. What I think is that it would be better if 
we could chouse the pulling direction ( -z or +z ) for each pulling group, 
instead of considering a reference group and chouse a "from_reference" 
or "to_reference" parameter to define this directions. Maybe in your case in 
which you are dealing with two groups separating one from each other, it might 
be confusing which is the reference group for each of each of the pulling 
groups, if I understood it correctly. 
I'm adding to this mail part of what I sent to Justin in reference to the pull 
option. It might be of any help to you or anyone else working on this: 

"We are attaching the pull.pdo file of this simulation. From this file we 
obtain the pulled_group_position (first column) and the spring_position (second 
column) so we calculate the force as: 

spring_elongation = [pulled_group_position( t) - spring_position (t)] - 
pulled_group_position( t = 0),
force = spring_elongation * k  

since the spring_position is always initially at the origin and the force 
should be zero at t = 0.  

Since we have developed our own program where so far can do afm simulations in 
an effective medium, we try to compare our simulations with the Gromacs' using 
the same approach. When we do so, we set the parameter 'nstcom' = 0 (in 
the .mdp file) but it was not accepted (only -1 is compatible in effective 
medium simulations). We did not encounter this problem in the hydrated system. 
This is important because removing the kinetic energy by controlling the center 
of mass velocity, will affect the dynamic behavior of the system and it will 
interfere in the determined force value.  

By the way, the improvements mentioned by Baaden are quite important and it 
would be great if you could take them in consideration, though he got a 
different way to determine the force, which I would like to discuss with him to 
see his point of view". 
Will keep in touch, 

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