[gmx-users] Steered Molecular Dynamics for citrate channel

[Bruna Franciele]

Dear gromacs users

I want to force the citrate to cross the channel using SMD, but when I run
the tutorial Umbrella Sampling for my system adapting the entries mdp for
gromacs-5.0.5 my results are staying bad!!

I want see citrato crossing the channel, and in the "generating
configurations" the citrate is in left of channel and  then right side of
channel.
How I can run this SMD protocol?

I'm using the entry mdp file for pull code:

; COM PULLING
pull = umbrella
pull_geometry = direction
pull_dim = Y N N
pull_start = yes
pull-print-reference = no
pull_nstxout = 1000
pull_nstfout = 1000
pull_ngroups = 2
pull-ncoords = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull-group1-name = Protein ; ref
pull-group2-name = CIT ; pulled
pull-coord1-groups = 1 2
pull-coord1-origin = 0 0 0
pull-coord1-vec = 1 0 0
pull-coord1-init = 0
pull-coord1-rate = 0.0
pull-coord1-k = 1000


Someone can help me, please??

Bruna.

Bruna Franciele Faria
-Laboratory of Molecular Dynamic and Simulation
UFSJ - Brazil