Dear Amber Users,
I am using the following script to drive a residue in a loop towards a +ve
charge pocket comprising of three residues. The initial LCOD is 55angstroms and
I want the final to be around 15ang. I have a few questions related to this run
which are listed pointwise.
Sample pulling input
&cntrl
imin=0, ntx=5, irest=1,
nstlim=1000000, dt=0.002,
ntc=2, ntf=2, tol=0.000001,
cut=10.0, ntb=2, ntp=1, taup=2.0,
igb=0,
ntpr=100, ntwx=500, ntwr=10000,
ntt=3, gamma_ln=2.0,
ig = 256259,
tempi=300.0, temp0=300.0,
/
ncsu_smd
output_file='smd.txt'
output_freq=10
variable
type=LCOD
i=(91,1644,91,1947,91,2247)
r=(1.0, 1.0, 1.0)
path=(X, 15.0) path_mode=LINES
harm=(10.0)
end variable
end ncsu_smd
Questions:
1. I understand the LCOD = distance between all three pairs combined using the
constants listed in r which are all 1.0 in my script. Is this correct ? So the
final LOD should be approx the sum of the three distances between the respective
pairs ?
2. I looked into the amber mailing list
(
http://archive.ambermd.org/200806/0150.html) and in this case is the pulling
velocity = 55-15/2ns = 20ang/ns ; 55 ang being my starting LCOD?
3. I am keeping the spring const throughout the run using harm=10. Is the unit
kcal/mol ang^2 ? If so how is it related to the pulling velocity and thermal
fluctuations ?
4. Is it possible to steer loops in two subunits of a dimeric protein
simultaneously. This would essentially mean using the above script
simultaneously for both subunits. I am confused if this can be done.
5. I think this script is implementing a const force smd as I fix the value of
harm. Is this true ?
I would eagerly look forward to your reply as I do not plan to start calculation
until I understand the details. Also it would be immensely helpful if you can
direct me to some reading material that explains the different principles
(const. vel smd and const. force smd) in details. Thanks a lot in advance.
Best Regards,
Moitrayee
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Received on Mon Jun 24 2013 - 21:00:04 PDT
