[gmx-users] About COM pulling

[Justin A. Lemkul]

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
> 
> 
>  
> 

-- 
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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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