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Dear GMX
users,
I am simulating the hydrophobic interaction between two 42-aminoacid
oligopeptides in pbc conditions with acqueous explicit solvent
with all-bonds constraints (LINCS).
In order to allow them to interact -for the first time- I am using
pull code.
My pull.ppa is
as follows
verbose = no
runtype = afm
group_1 = protein_2
reference_group = protein_1
reftype = com_t0
reflag = 1
pulldim = Y Y Y
Supposing that in my
sistem the two proteins (interacting groups) are distant 50 nm at time 0 and I
would like to cover this distance in about 2000 ps.
Should I use
an
afm_rate1 = 0.025 (50ns/2000ps)?
Can anyone suggest
me the force constant value to simulate the hydrophobic
interaction (afm_k1) ?
How can I set the unit
vector describing the direction of pulling (afm_dir1) ?
May I set
the initial position relative to the reference group as
afm_init1 = 0 0 0
I am using GROMACS 3.2.1, does pull
code work in parallel?
Sorry for the long message and I hope
someone would help me.
Thanks in advance.
Marino
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