On 4/19/20 4:25 PM, lazaro monteserin wrote:
I thought this approach initially because I will refine the calculations
later at DFT level. What do you think?
If you need a QM reference state for subsequent geometry refinement,
just generate the QM-optimized geometry and start your calculations from
that. You can then do an energy minimization with the force field to
determine how well the molecular mechanics approximation agrees with QM
(perhaps not very well as most nucleic acid force fields have not used
DFT methods in their derivation).
-Justin
On Sun, Apr 19, 2020 at 5:17 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 4/19/20 4:12 PM, lazaro monteserin wrote:
Dear Dr. Lemkul you are completely right. But then how could I approach
this problem to get an answer at the end that make sense?
What is the purpose of requiring that the simulation start from the most
stable vacuum conformation? There are very few rotatable bonds in a
nucleoside and they are likely capable of fairly exhaustive sampling in
water, anyway. The force field isn't designed for vacuum so anything you
generate is likely to either be irrelevant in water or otherwise easily
accessible in water in the first place.
-Justin
On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 4/18/20 7:39 PM, lazaro monteserin wrote:
Dear Gromacs users,
As I have referred before I am simulating small molecules (nucleosides)
(around 33 atoms) in vacuum in Gromacs. When I do the simulations at
the
end I want to select the most stable structure from the trajectory for
the
next steps.
What would be the best methodology to use to run a molecular dynamics
for
this?:
1) Run an anneling and collect the different frames for the trajectory
and
then at the end analyze the RSMD, free energy and maybe do clustering
for
the different frames to select the most stable structure?
How do you propose to compute the conformational free energy? Note also
that no biomolecular force field is validated for use in the gas phase,
so the balance of conformational sampling has no guarantee of being
physically meaningful.
2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella
sampling"?, the only problem here is that I want all dihedral angles to
rotate and I do not know how to do this.
You can enforce dihedral rotation with the pull code, but the tutorial
has little use here aside from general concepts.
3) Do a procedure similar to tutorial 6 "Free energy of solvation" in
which
I generate the free energy from different lambda values from
consecutive
simulations.
The tutorial is for decoupling a solute from water. You have a molecule
in vacuum. The only thing to decouple is the molecule itself, which will
give you an annihilated, physically nonsensical structure.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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