[gmx-users] pulling test

Marco Deriu marcoagostino.deriu at fastwebnet.it
Fri Jan 20 17:57:14 CET 2006

Hi Gromacs-users

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

; Directions

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 

                                                                                                                                                           Marco D
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