[gmx-users] about COM pulling and g_dist

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Oct 5 14:35:22 CEST 2010

Dear Zhongjin:

1. You have indeed provided more data, but please try to make some  
progress on your own. E.g. you tell me the order of selections into  
g_dist, but you should try reversing the order.

2. Your figures are difficult to interpret -- I only opened Snap5, but  
I don't know what part of your procedure this is from.

3. I'm not going to download 4 separate files, rename them, look at  
them, and try to figure out what they mean. If you want more help,  
please provide good descriptions on all figures and upload them to  
some file storage site where I can look at them online (e.g.  
photobucket, flikr).


-- original message --

--- 10?10?5????, zhongjin <zhongjin1000 at yahoo.com.cn> ???

> ???: zhongjin <zhongjin1000 at yahoo.com.cn>
> ??: about COM pulling and g_dist
> ???: gmx-users at gromacs.org
> ??: 2010?10?5?,??,??9:53
>  Dear Chris,
> Snap7.jpg shows distance in one umbrella sampling window.
>  Zhongjin He

Dear Zhongjin:

First, I see no reason why you would not expect your g_dist values to
be negative. If you want the positive distances, then reverse the
order of the groups as you pass then to g_dist. Also, what type of
values do you get directly out of mdrun and into the pull_x.xvg file?

Second, how did you go from values to a PMF? did you use wham? If so,
and if you gave a succession of increasing value positive numbers to
note restraint positions and then your values you passed were
increasingly negative, then you will certainly get the wrong PMF.

Third, your lack of symmetry may just be a lack of convergence. Have
you done and convergence tests?

If this doesn't solve it and you want more help, please post your
g_dist commands and post an image of your pmf online.


-- original message --

Hi all,
      I have done a simulation about pulling a K+ throug a (9,9)CNT.
The results may be strange.
      The length of the CNT is 1.477nm,the box is 5*5*5nm.I use the
Umbrella Sampling to calculate PMF ,following the tutorial by Justin
A. Lemkul. I have pulled (along Z direction) a K+ (pulling group)frome
one end (reference group ) of the CNT to another end to generate
Configurations for Umbrella Sampling,both ends of CNT were fixed. Then
I use g_dist to calculate the COM distance between K+ and the
reference group,the result is strange,the Z direction component -dz is
negative,it should be positive,because the Z coordinate of K+ is lager
than that of reference in the .xtc output file. I don't know why. the
pulling distance is not larger than half of the box size.the Z
direction component -dz  is also negative in Umbrella Sampling windows.
     Then do Umbrella Sampling,the pulling group and reference group is
as in COM pulling step.pull_geometry = distance,pull_rate = 0. The PMF
is negative and not symmetry about the middle of the CNT.I think it is
wrong.May be it is because the dz is negative,or the choice of
reference is not proper, it should be the middle the CNT as the
reference.Anybody could help? Thanks a lot!
; Pull type: no, umbrella, constraint or constant_force
pull                     = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry            = distance
; 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             = 500
pull_nstfout             = 500
; Number of pull groups
pull_ngroups             = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
pull_group0              = refer
pull_weights0            =
pull_pbcatom0            = 0
pull_group1              = K
pull_weights1            =
pull_pbcatom1            = 0
pull_vec1                = 0 0 0
pull_init1               = 0
pull_rate1               = 0.0
pull_k1                  = 1000

Zhongjin He

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