[gmx-users] Gromacs 5 umbrella sampling

[Andres Ortega Guerrero]

I'm sorry Justin, My mistake, 

when i use this pull code, using grompp, with this pull code

; Pull code
pull            = umbrella
pull_geometry   = direction  ; 
;pull_vec1       = 0.0 0.0 1.0 ; 
pull_coord1_vec       = 0.0 0.0 1.0 ; 
;pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_coord1_init      = 0.0
pull_ngroups    = 1
pull-coord1-groups = 0 1 
pull_group0_name    = protein2pull
pull_group1_name    = DOX 
;pull-r1         = 1.0 
;pull-r0         = 1.0 
pull_coord1_rate      = 0.0      ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k         = 800     ; kJ mol^-1 nm^-2
;pull_k1         = 800     ; kJ mol^-1 nm^-2

this is the error 

Pull group  natoms  pbc atom  distance at start     reference at t=0
       0         0         0
       1        68     57366 
-------------------------------------------------------
Program grompp, VERSION 5.0-beta2
Source code file: /home/bionano/Desktop/gromacs-5.0-beta2/src/gromacs/pulling/pull.c, line: 337

Fatal error:
Distance between pull groups 0 and 1 (8.777763 nm) is larger than 0.49 times the box size (5.774220)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

but the problem is that hi is assuming 0 as the system, but i want to use as in gromacs 4.6.5 group0 as protein2pull, define in my index file,
which is in an appropriate distance, and if i use the index number from the index file in the coord1-group. it appears that the must be between 0-3 
The initial configuration where made in gromacs 4.6.5 and the index file too

Thank you in advance