[gmx-users] Question on pullcode

[Semen Esilevsky]

Last year I also tried the pull code. I had to measure
the mean force acting on certain group. I've found
that this code doesn't work as expected and asked
about this problem, but there where no answer. It
seems that nobody can explain in details how it
works...

--- Xu Zhiping <xzp02 at mails.tsinghua.edu.cn> wrote:
> Dear All:
>       I am constructing a 1d PBC simulation by
> pullcode, the system
> contains two groups GRP1(fixed on the periodic
> direction by
> "freezegrp"), and GRP2(which I want to applied a
> "constant velocity" by
> pulling).
> 
>  
> ---------------------------GRP1
>  
> ---------------------------GRP2  ->V
>  
> |<--------PBC---------->|
> 
>      So I write a pull.ppa file as following:
> -------X
> verbose              = no
> runtype              = afm
> group_1             = GRP2
> 
> reference_group = GRP1
> reftype              = com
> reflag                = 1
> pulldim             = N N Y
> 
> afm_rate_1       = 0.1        ; nm/ps
> afm_k1            = 10000	  ;kJmol^(-1)nm^(-2)
> afm_dir1           = 0 0 1
> -------X
>      But when I use g_traj to check out the
> veloctity of COM of GRP2, I
> found that the velocity of GRP2 is increasing, not
> equal to the pull
> rate, can anyone help me with this? The purpose of
> my work is to apply a
> constant velocity to GRP2 related to GRP1 in a PBC
> system.
> -------X
> # This file was created by g_traj
> # which is part of G R O M A C S:
> # Gromacs Runs On Most of All Computer Systems
> # All this happened at: Sat Jun 26 10:45:51 2004
> #
> @    title "Center of mass velocity"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Velocity (nm/ps)"
> @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 "GRP2 X"
> @ s1 legend "GRP2 Y"
> @ s2 legend "GRP2 Z"
>  0      0       0       0
>  0.05   -2.59307e-05    0.000141022     0.000123713
>  0.1    -3.10929e-05    0.000345674     0.000682453
>  0.15   -1.78149e-05    0.000370906     0.00161342
>  0.2    5.0185e-05      0.000164425     0.00289621
>  0.25   6.73612e-05     7.31421e-05     0.00458163
>  0.3    0.000114233     -4.77369e-05    0.00661946
>  0.35   0.000163221     -0.000229757    0.008967
>  0.4    0.000155464     -0.000285763    0.0117026
>  0.45   0.000110269     -0.000148486    0.0147423
>  0.5    4.86949e-05     -4.15635e-05    0.018137
>  0.55   3.70799e-05     4.25482e-05     0.021802
>  0.6    5.68639e-05     0.000279603     0.0257509
>  0.65   8.86486e-05     0.000395579     0.030018
>  0.7    0.000111812     0.000293992     0.0345183
>  0.75   0.000140816     0.000190741     0.0392723
>  0.8    0.000152404     0.000137144     0.0442746
>  0.85   0.000177164     -6.62569e-05    0.0494933
>  0.9    0.000197134     -0.000311002    0.0549318
>  0.95   0.000145792     -0.00026576     0.060511
>  1      9.85206e-05     -0.000224874    0.0662472
> ......
> -------X
> 
> Best,
> ZP
> ---------------------------------------------
> Xu ZhiPing
> Ph.D Candidate
> Office: 3-405
> Tel    : +86-10-627-83814
> Department of Enginnering Mechanics
> Tsinghua University
> Beijing, CHINA, 100084
> ---------------------------------------------  
> 
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