[gmx-users] about COM pulling and g_dist

zhongjin zhongjin1000 at yahoo.com.cn
Mon Oct 4 12:25:57 CEST 2010

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!
; COM PULLING          
; 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), kJ/(mol*nm^2)
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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