[gmx-users] Remove COM of a group or of the whole system

[Xiaohua Zhang]

Dear all,

I have met a problem in my simulation, where I hope to remove the
center of mass of one group, namely CNT02, and to pull another group
by a constant force. My mdp file reads:

;       Remove center of mass translation
comm_mode           =  Linear
nstcomm             =  10
comm_grps           =  CNT02
;       COM pulling
pull                =  constant_force
pull_geometry       =  direction_periodic
pull_ngroups        =  1
pull_group1         =  CNT05
pull_vec1           =  0.0 0.0 1.0
pull_k1             =  10   ;  kJ / mol / nm

The COM pulling has worked, as the Z position of CNT05 was
continuously increasing/decreasing along the force direction. However,
I found the program has removed the COM of the whole system, rather
than of the group CNT02.

Let me use "g_traj -com -ox coord.xvg" to extract the COM information,

Group     0 (         System) has 57608 elements
Group     1 (          Other) has 57608 elements
Group     2 (          CNT01) has  3032 elements
Group     3 (          CNT02) has  3032 elements
Group     4 (          CNT03) has  3032 elements
Group     5 (          CNT04) has  3032 elements
Group     6 (          CNT05) has  3032 elements
Group     7 (          CNT06) has  3032 elements
Group     8 (          CNT07) has  3032 elements
Group     9 (          CNT08) has  3032 elements
....

If 0 was selected, such coord.xvg was generated
@    title "Center of mass"
@    xaxis  label "Time (ps)"
@    yaxis  label "Coordinate (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 "System X"
@ s1 legend "System Y"
@ s2 legend "System Z"
 0      10      10      17.3113
 0.2    10      10      17.3113
 0.4    10      10      17.3113
 0.6    10      10      17.3113

If 3 was selected, for CNT02, the COM was not a constant, i.e., CNT02
was moving all the time.
@ s0 legend "CNT02 X"
@ s1 legend "CNT02 Y"
@ s2 legend "CNT02 Z"
 0      11.7971 10.2633 17.5756
 0.2    11.7966 10.2602 17.5768
 0.4    11.7928 10.2594 17.5783
 0.6    11.789  10.2582 17.5799
 0.8    11.7856 10.2552 17.5817
 1      11.7831 10.2547 17.5837
 1.2    11.7828 10.2554 17.586
 1.4    11.7846 10.2562 17.5884
 1.6    11.7891 10.2582 17.5909
 1.8    11.7942 10.2621 17.5934


Best Regards
xiaohua

-- 
Xiaohua Zhang

Suzhou Institute of Nano-Tech and Nano-Bionics
Ruoshui Road 398, Suzhou 215123, China

Phone: +86 512 62872552
Mobile: +86 137 71904040
Email: zhangxh at fudan.edu.cn
Email: xhzhang2009 at sinano.ac.cn