On Sat, Jun 29, 2013 at 1:52 AM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> Thanks again for your reply.
>
> In the previous mail you suggest to use rstwt = -1.0, 1.0; can I use
> another value for the same. The -1 and 1 indicates that simple difference
> of two separation, if I use 2.0 then it will be difference of double
> separation. Am I right?
>
-2.0, 2.0 is functionally equivalent to -1.0,1.0, so there's not much point
in 'doubling' IMO. -2.0,1.0 is a different reaction coordinate (and may be
preferable if the first reaction coordinate is expected to change only half
as much as the second reaction coordinate, for instance).
If you use 2.0 for both, then that generalized distance would double as
well, yes. (I encourage you not to think of the generalized distance as a
'separation', since it's a linear combination of two separations).
I think by using (x_2 - x_1) you indicate the separation between atom1 and
> atom2. But in the input I have to specify r1, r2, r3, r4; which is the
> difference of separation, but what will be the value of individual
> separation?
>
r1, r2, r3, and r4 are points in the flat-well potential. They correspond
not to separations, but to the value of the generalized distance restraint.
The values I gave in my example
LCOD of 2 distances
&rst
iat=1,2,3,4, rk2=5.0, rk3=5.0, r1=-10, r2=0, r3=0, r4=10, rstwt=-1.0,1.0,
/
correspond to a
harmonic potential with a force constant of 5.0 kcal/mol (in the energy
equation U=k(x-x_0)^2 -- there is no 1/2 factor) that is harmonic between
-10 and 10 with the center of the potential at 0. The generalized
coordinate is zero when the 2--1 separation is equal to the 3--4
separation.
Note that a generalized distance restraint imposes a single restraint on
two degrees of freedom. In general, a single value of the generalized
restraint cannot be broken down into specific individual separations.
There are an infinite number of individual separations that can yield a
specific value for their linear combination. For instance, if 1--2 were
separated by 2 Å and so was 3--4, the generalized coordinate would have a
value of 0. Likewise if both were separated by 1 Å. If you want to
control both coordinates independently, you will need to specify two
restraints and generate a free energy surface using 2D-WHAM.
> Actually, in my case one H-atom is bonded with one N-atom and during the
> reaction the H-atom will shift towards another O-atom. I want to increase
> the N-H bond length and decrease H-O separation and set the reaction
> coordinate as the difference of two separation. So my doubt is that if I
> specify the r1, r2... (difference of separation) then two separation with
> change simultaneously, or it will change only one.
>
They will change simultaneously in the way that minimizes the energy (in
principle).
>
> It is not clear to me what is the difference in sander and pmemd?
>
This is described in the Amber manual. sander and pmemd give the same
answers for the same input, in general. But pmemd does not support all of
the features that sander supports. Therefore, since pmemd fails when rstwt
is added to the &rst namelist, that means that pmemd does not support LCOD
restraints, and you have to use sander.
In general, pmemd is ~2x faster than sander on a single core (in explicit
solvent), and the parallel scaling is much better. As a result, when a
feature you want is implemented in pmemd, you should use that program.
(But when it's not, you must stick to sander)
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Jun 29 2013 - 06:30:03 PDT
