Dear All,
I've simulated a protein in order to back up some experimental data
regarding the importance of a Tyr residue. This residue is part of a loop
that has an open/close type motion. The study began because the difraction
structure showed that this Tyr is quite different from other structures
known in the literature. With MD we have been able to see that this Tyr
residue does something close to a pendulum motion. It prefers some
configurations over others, meaning, it prefers either to be facing the
catalytic center or it prefers to face the opposite way. This hinge motion
is associated with changes in the loop conformation and it seems that the
outward/inward positions are related to the phi/psi dihedral angles of this
particular residue (or a neighboring residue, we are still not sure). I've
worked with umbrella sampling before in amber, but I would like to use the
abmd suite to calculate the relative free energy differences between these
two configurations.
I've started following TUTORIAL A31, specifically part 1 (Calculating 2-d
free energy landscapes for a di-alanine peptide), but I am having some
trouble figuring out some things.
First, as a test run, I've adapted the files from the tutorial in order to
describe the two TORSIONS I would like to sample. The mdin abmd variables
are set as:
&abmd
mode = 'FLOODING'
timescale = 1.0
monitor_freq = 500
monitor_file = 'abmd_monitor_1.dat'
cv_file = 'cv.in'
umbrella_file = 'bias_1.nc'
selection_freq = 5000
selection_constant = 0.00001
selection_epsilon = 0.0
wt_temperature = 10000
wt_umbrella_file = 'wt_bias_1.nc'
And the collective variable file 'cv.in' is:
&colvar
cv_type = 'TORSION'
cv_ni = 4
cv_i = 4270,4272,4274,4291 !phi
resolution = 0.2
cv_min = -1.40
cv_max = 1.40
/
&colvar
cv_type = 'TORSION'
cv_ni = 4
cv_i = 4291,4272,4274,4303 !psi
resolution = 0.2
cv_min = -0.7
cv_max = 0.7
/
There are some things I would like to ask though. First, I've used the
cv_min and cv_max to specify that I would only like to sample torsion
values that ranges from the maximum and minimum values I observed in the MD
simulation. Is that necessary, or even good practice?
For this test, I am running only 2 replicas. From the tutorial, I could see
that the wt_bias_#.nc files are equal (I've used cmp wt_bias_1.nc
wt_bias_2.nc). So, it would not matter which file I choose for post
processing with nfe-umbrella-slice, correct?
The manual states that choosing the best selection_constant is somewhat of
an art form. Can you suggest some literature (or point it out explicitly)
as to how I would choose the best values for my simulations?
Thank you
Fabrício Bracht
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Received on Tue Jun 13 2017 - 14:00:02 PDT
