Dear All:
I am trying to use steer molecular dynamics simulations to pull a
ligand along a channel pore (along the Z axis) by constant rate. I
know how to realize this by GROMACS3, however, it seemed that in
gromacs4, there are some changes regarding this issues, so I am
pasting my pull code parameters and some of my questions here, Could
any one be so kind to answer my questions? Thanks in advance.
My pull code parameters
---------------------------------------
pull = umbrella
pull_dim = N N Y
pull_start = yes
####### if the pull_start is set to "yes", it means that, the distance
between the pull group and the reference group of the starting
structure will be calculated and the value will be added to the
pull_init1 and the final result will be used a the inital distance
between the pull group and the reference group in the simulations, am
i right?###########
pull_nstxout = 500
####### if the pull_nstxout is set to 500, the COM of the pull group
will be write every 500 steps (i.e. 1ps,if the time step is
2fs)?############
pull_nstfout = 500
pull_group0 = Protein
pull_group1 = Ligand
pull_vec1 = 0 0 1
pull_init1 = 0
pull_rate1 = 0.025
pull_k1 = 1000
############how can I make sure the pull_rate1 and the pull_k1 I used
is appropriate?###############3
__________________
############ what is the out put of the pulling code? #############
Does the above parameters can pull the ligand along the Z axis with a
constant rate successfully? Are there any problem the my pull code
parameters?
Thanks very much for your time and your kind!
Best Regards
R.-X. Gu
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