[gmx-developers] pulling three molecules into a membrane by constrainting

[Yukun Wang]

Hi all:
    I want to pull three small molecules into a membrane along three vectors
perpendicular to it by constrainting, the parameter setting is below:
pull                     = constraint
pull_constr_tol          = 1e-5
pull_geometry            = position
pull_dim                 = Y Y Y
pull_start               = yes
pull_nstxout             = 50
pull_nstfout             = 50
pull_ngroups             = 3
pull_group0              = lipid            ; reference group
pull_group1              = phe1
pull_vec1                = 0 0 -1
pull_rate1               = 0.0002             ; [nm/ps]
pull_group2              = phe2
pull_vec2                = 0 0
-1
pull_rate2               = 0.0002             ;
[nm/ps]
pull_group3              = phe3
pull_vec3                = 0 0 -1
pull_rate3               = 0.0002             ; [nm/ps]

 But I get an error :

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2465.976683, max 48465.484375 (between atoms 8716 and 8715)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   8777   8776   82.5    0.1470 123.6644      0.1470
   8775   8776   97.3    0.1530 1185.9658      0.1530
   8774   8775   66.1    0.1530 1091.0201      0.1530
   8773   8774   96.5    0.1390 11850.9688      0.1390
   8771   8773   81.2    0.1390 22400.8809      0.1390
   8771   8772   92.8    0.1890 19976.3652      0.1890
   8770   8771   93.0    0.1390 22574.0859      0.1390
   8769   8774   41.7    0.1390 866.0833      0.1390
   8768   8769  160.1    0.1390 693.7319      0.1390
   8768   8770   79.8    0.1390 4601.1436      0.1390
   8767   8768   99.9    0.1431 1037.8502      0.1430
   8780   8777  109.1    0.1000  20.7450      0.1000
   8779   8777  118.4    0.1000  20.6520      0.1000
   8778   8777  107.8    0.1000  21.5070      0.1000
   8746   8745   81.2    0
...
Wrote pdb files with previous and current coordinates
step 0
rank 5 in job 1  c0201_60409   caused collective abort of all ranks
  exit status of rank 5: killed by signal 11
rank 3 in job 1  c0201_60409   caused collective abort of all ranks
  exit status of rank 3: killed by signal 11
rank 1 in job 1  c0201_60409   caused collective abort of all ranks
  exit status of rank 1: killed by signal 11


I don't know where is the error coming from? I test the same system by
umbrella pulling, it works well with the parameter as below:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull                     = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry            = position
; Select components for the pull vector. default: Y Y Y
pull_dim                 = Y Y 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                  = 1.5
pull_constr_tol          = 1e-06
pull_start               = yes
pull_nstxout             = 50
pull_nstfout             = 50
; Number of pull groups
pull_ngroups             = 3
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0              = lipid
pull_weights0            =
pull_pbcatom0            = 0
pull_group1              = phe1
pull_weights1            =
pull_pbcatom1            = 0
pull_vec1                = 0 0 -1
pull_init1               = 0.0 0.0 0.0
pull_rate1               = 0.00005
pull_k1                  = 500

pull_group2              = phe2
pull_weights2            =
pull_pbcatom2            = 0
pull_vec2                = 0 0 1
pull_init2               = 0.0 0.0 0.0
pull_rate2               = 0.00005
pull_k2                  = 500

pull_group3              = phe3
pull_weights3            =
pull_pbcatom3            = 0
pull_vec3                = 0 0 1
pull_init3               = 0.0 0.0 0.0
pull_rate3               = 0.00002
pull_k3                  = 500
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