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
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