zhongjin wrote:
Hi all,
I am using GMX4.5.1 to do COM pulling .
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry = direction
; Select components for the pull vector. default: Y Y Y
pull_dim = N N Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0 = 1
pull_constr_tol = 1e-06
pull_start = yes
pull_nstxout = 10
pull_nstfout = 1
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0 = refer
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = K
pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 = 0.0 0.0 1.0
pull_init1 = 0.0
pull_rate1 = 0.001
pull_k1 = 1000
pull_kB1 =
I don't know why it did not pull in Z direction? And what
does pull_start = yes mean?
You may not be getting a large displacement because you have a slow pulling rate
(0.001 nm/ps). There's nothing wrong with it, but if you're running a rather
short simulation, that may be insufficient to cause noticeable displacement,
depending on the forces that your pull group is experiencing.
Please refer to the manual for the interpretation of pull_start (and any other
settings, for that matter).
http://manual.gromacs.org/current/online/mdp_opt.html#pull
All of these settings are also described in the COM pulling tutorial.
http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
-Justin
Thanks !
Zhongjin He
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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