[gmx-users] pullx file content with pull_geometry = position

[Bastien Loubet]

Dear gromacs user,

I run a simulation where I restrain two groups in a specific position with
respect to one another: one is part of a protein (index group name:
pull_group) the other is just one ion (index pull_group name r_60022).
I have the following parameters in my mdp file:

*********************************
; Pull code
pull            = umbrella
pull_geometry   = position   ;
pull_dim        = Y Y Y
pull_start      = no
pull_ngroups    = 1
pull_group0     = pull_group
pull_group1     = r_60022
pull_init1      = -.4110 1.0700 1.7760
pull_rate1      = 0.0
pull_vec1       = -0.264 0.315 0.912
pull_k1         = 1000      ; kJ mol^-1 nm^-2
pull_nstxout    = 100      ; every 0.2 ps
pull_nstfout    = 100      ; every 0.2 ps
**********************************

So the ion should be restrained around the position pull_init1 with respect
to the center of mass of the protein.
Here is a sample of the obtained pullx.xvg file:

**********************************
@    title "Pull COM"
@    xaxis  label "Time (ps)"
@    yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 X"
@ s1 legend "0 Y"
@ s2 legend "0 Z"
@ s3 legend "1 dX"
@ s4 legend "1 dY"
@ s5 legend "1 dZ"
0.0000  3.43102 5.2156  11.5301 -0.531018       1.0244  2.13988
0.2000  3.43096 5.21543 11.53   -0.544007       1.02157 2.14952
0.4000  3.43094 5.2146  11.5304 -0.551138       1.00177 2.12238
0.6000  3.43074 5.21354 11.5312 -0.559285       1.01417 2.13649
(...)
20.0000 3.45331 5.22215 11.51   -0.646908       0.939066        2.11768
(...)
40.0000 3.45141 5.21115 11.5685 -0.689742       0.978908        2.14589
(...)
*****************************************

As far as I understood the manual and after searching the forum I though
that the first column is the time, the next three columns the position of
the pulled group (r_60022) at the time and the last three columns the
distance in the x y z direction between the reference group (pull_group, bad
name choice I know) and the pulled group (r_60022). If that was true it
would suggest that the ion is pulled more than three A away from the center
of the umbrella potential.
After checking the trajectory visually and by calculating the distance
between pull_group and  r_60022 using g_dist on the trajectory we can see it
is not the case. Here is a sample of the g_dist output:

****************************************
@    title "Distance"
@    xaxis  label "Time (ps)"
@    yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
   0.0000000    2.1085827   -0.3782945    1.1350875    1.7362576
  20.0000000    2.0527425   -0.4464533    1.0719213    1.6927538
  40.0000000    2.1132109   -0.3499784    1.1239562    1.7549639
(...)
***************************************

Which oscillate correctly around the pull_init1 vector as defined in the mdp
file.

More importantly these results are different from the results in the
pullx.xvg file (at least the results I expected to have).

Can somebody clarify what is actually in the pullx.xvg file ?

Best,

Bastien Loubet



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