[gmx-users] pulling test
marcoagostino.deriu at fastwebnet.it
Fri Jan 20 17:57:14 CET 2006
I'm trying to do a pulling test in a tubulin protein.
I defined pull and reference groups each composed by more than 15 atoms.
The recence group is frozen during all simulation.
My .ppa file is
verbose = yes
runtype = afm
group_1 = pull
reference_group = reference
reftype = com
pull_dim = Y N N
; rate in nm/ps
afm_rate1 = 0.1
; Force constants in kJ/(mol*nm^2)
afm_k1 = 3000
afm_dir1 = 1.0 0.0 0.0
; COM (= pull group's COM)
afm_init1 = 12.262807 4.368293 4.509590
During the simulation I have noticed that the centre of mass of the pull group (pull) can also move in opposite sense respect to afm_dir1 (user-defined).
In the other hand if I have defined afm_dir1 = 1.0 0.0 0.0 the pull group, during the pulling test, can move in direction -1.0 0.0 0.0.
Can this depend on the value of spring elastic constant or on the afm_rate value?
Another question is about the .pdo file.
Why in Gromacs 3.2 the COM value of the reference group is allways set to 0.0, in pdo file?
Thanks a lot
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