On Wed, Oct 27, 2010 at 08:41:05AM +0400, subrata paul wrote:
> Dear sir
>
> Can we ues packmol program for generating intial structure for Simulation in
> AMBER10. After simulation from which file we can plot radial distribution
> function and how we do this.please help me.
>
>
> thanking you
> subrata paul
Yes, packmol works, but you will have to be aware of a couple of
things:
1. When you create the prmtop and inpcrd files for the first
simulation, set a box for the system so that the simulation programs,
sander and pmemd, know you are simulating a periodic system. See
the tleap/xleap documentation.
2. If you use the recommended default parameters for packmol,
the initial structure may have a very high vdw energy. You can work
around this, although sometimes it is painful: Do several sequential
short minimizations (I use 10 step) and use the generated restart file
of one minimization as the coordinate input file for the next
minimization. I have had to do as many of 7 of these short runs
before the system is energetically satisfactory enough to do a longer
minimization without crashing. I routinely use 500 steps in the final
minimization.
3. Start equilibrating the system with an extensive NPT dynamics
run.
You may want to preceed this with a NVT run to ramp up the
temperature, although in my experience the NVT run can be often
bypassed by using a Langevin thermostat if the NPT run is long enough.
Additional comments on this aspect are welcomed.
As to why a longer than normal initial NPT run is a good idea, first
you need to equilibrate the density. This is always needed. Second,
think about the water H-bond network. (I am assuming you want a box
of water, but this consideration holds for any polar solvent.)
Packmol does not create the H-bond network since the waters are
randomly oriented. The packmol algorithm has no notion of energetics
or even of force fields. It is just packing hard spheres. Creating a
system with LEaP solvent boxes results in a system in which a large
portion of the solvent has been equilibrated, but the packmol system
must be equilibrated for a long enough time to generate the H-bonding
network / water clusters. For simple water or mixed solvent boxes
and/or systems with small solutes (e.g., alanine dipeptide), I use a
5ns NPT simulation for an initial equilibration. Follow this up with
an analysis for proper equilibration as outlined on this email list
and in the literature.
Can someone with water rotational relaxation time foo enlighten us on
the expected dynamics of this effect?
If all you want is a solvent box to calculate radial distribution
functions, why don't you generate it in LEaP by solvating a single
solvent molecule with the appropriate equilibrated solvent box? This
is a much more straightforward approach than using packmol. You still
need the NPT simulation to equlibrate the density, but can often get
away with using a shorter run than needed for packmol systems.
I would appreciate anyone else's comments on these methods to generate
initial systems for simulation. In the near future I want to post to
the list some hints on using these kinds of set up methods. I would
like to include more than just my ideas.
HTH,
Bud dodson
--
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email: mldodson-at-comcast-dot-net
Phone: eight_three_two-56_three-386_one
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Received on Wed Oct 27 2010 - 08:00:03 PDT
