Dear Amber Users,
This is in reference to the tutorial at
http://enzyme.fbb.msu.ru/Tutorials/Tutorial_3/
Questions:
1. I understand the LCOD mode was supported in ncsu_smd module which is no
longer supported by Amber mailing list. Is there an equivalent when I am using
the jar=1 option. This is because I want to have parallel restraints and move an
atom close to a set of three atoms.
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 and 15 being the
endpoint ?
3. I am keeping the spring const throughout the run using rk2=1.0725. Is the
unit kcal/mol ang^2 ? If so how is it related to the pulling velocity and
thermal fluctuations ? Also what is the physical meaning of this value ?
4. Is it possible to steer loops in two subunits of a dimeric protein
simultaneously. 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
spring constant. 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 Tue Jun 25 2013 - 12:30:02 PDT
