[gmx-users] Re: COM Pulling

Raj princecrusial05 at gmail.com
Sun Jul 1 06:02:25 CEST 2012

Dear Justin,

I've tried what you have suggested. I have used the pull code and gave 4
amino acid residues as a reference group. The location of the groups are one
below the ligand (in the protein core) and 3 were on the above ( towards the
active site gorge). When i used the code

pull                 = umbrella
pull_geometry  = distance  ; simple distance increase
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = DRG
pull_group1     = reference groups
pull_rate1       = 0.003      ; 0.01 nm per ps = 10 nm per ns
pull_k1           = 1000      ; kJ mol^-1 nm^-2

the ligand migrated more and more towards the protein , not coming out of
the protein through the channel i defined by referring the amino acid groups

when I tried with pull_geometry = position, the pull_vec i gave as 0 0 1 and
pull_initial = 0.1 but the grompp ends up with an error saying pull_vec can
not be zero.

when i was trying to use pull_geometry = direction the system blowed up. but
the pull_geometry = distance worked well.

please give me a suggestion to resolve the issue

View this message in context: http://gromacs.5086.n6.nabble.com/COM-Pulling-tp4998944p4998989.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list