On Tue, Jun 25, 2013 at 3:23 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> 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.
>
Yes, there is an equivalent (kind of). It only supports a subset of the
functionality provided by the NCSU module, but arguably some of the most
popular functionality.
Look for the 'generalized distance' restraint in Chapter 6 of the Amber
manual (the NMR restraint section). The relevant variables are iat and
rstwt. It lets you do a linear combination of up to 4 distances.
> 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 ?
>
Yes.
> 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 ?
>
Yes, it is kcal/mol/ang^2. However, the restraint equation is
U=k[f(s)-s_0] where s_0 is the 'equilibrium' value of the reaction
coordinate s and f(s) is the actual value of the reaction coordinate
(notice there is no factor of 1/2 in front of it).
This value is effectively twice the spring constant of the restraint.
There's no additional 'physical' meaning to this potential since it's a
biasing potential that's not real (and that you hope to remove later from
the final PMF).
> 4. Is it possible to steer loops in two subunits of a dimeric protein
> simultaneously. I am confused if this can be done.
>
Only if both 'steerings' are part of the same reaction coordinate. I
believe that only one coordinate can be steered at a time using the NMRopt
code.
5. I think this script is implementing a const force smd as I fix the value
> of
> spring constant. Is this true ?
>
I may not be familiar with how this terminology is used, but in general
this will NOT be constant force. It is constant force constant, but the
force itself will obviously change based on how far away from the
'equilibrium' value the conformation happens to be. I actually think
people call this 'constant velocity' steered MD since the center of the
steering potential is moved at a constant speed.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 25 2013 - 15:00:02 PDT
