[gmx-users] Question on pullcode

[Xu Zhiping]

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
---------------------------------------------