[gmx-users] hints for core/shell optimization?

Tamas Karpati tkarpati at gmail.com
Fri Aug 1 12:13:44 CEST 2014

Dear Justin,

>> If I have a Mg++ ion with q_D=+3.2 then for the shell particle I'd set
>> +3.2 and for the Mg atom I should stay with +2? So far -in order to maintain
>> charge neutrality of the system- I've been using -1.2 for Mg to have the
>> correct +2e for the AD duett. Big difference!
> Yes, the Drude and core atom will have charges of opposite sign to yield the
> total charge on the pair.  A positively charged auxiliary particle is a bit
> weird, but not wrong, if the model was parametrized that way.  Normally the

I've tried writing +2 charge for Mg in the TOP file and let GROMACS combine
it with the Drude charge of +3.2 but it has set a total charge of ca.
few thousands
e and induced a great movement of the shell particles. The average A-D
distance raised from ca. 0.01 to 0.3 nm! I consider the original solution
better (I pre-combine q_D with q_A and write q_C=q_A-q_D into the TOP file).

> The way I have done the exclusions is redundant and in principle not totally
> necessary.  Atom-Drude pairs connected via bonds or within [polarization]
> directives (e.g. 1-2 and 3-4) should already be excluded from one another,
> so in reality:
> [ exclusions ]
> 1 3 4
> 2 3 4
> should cover it.

I does, at least my job is functionally runs but MDRUN stops for too low
atomic displacements while forces are in the sky:

# Step=    2, Dmax= 5.0e-03 nm, Epot= -1.35892e+08 Fmax= 3.49164e+07, atom= 1242
# Step=    3, Dmax= 6.0e-03 nm, Epot= -1.72899e+08 Fmax= 8.98685e+08, atom= 1900
# Step=    7, Dmax= 9.0e-04 nm, Epot= -3.21500e+09 Fmax= 1.05629e+16, atom= 6794
# Step=   18, Dmax= 1.1e-06 nm, Epot= -1.33283e+09 Fmax= 1.08140e+14, atom= 679
# Energy minimization has stopped, but the forces have not converged to the
# requested precision Fmax < 0.1 (which may not be possible for your system).
# It stopped because the algorithm tried to make a new step whose size was too
# small, or there was no change in the energy since last step. Either way, we
# regard the minimization as converged to within the available machine
# precision, given your starting configuration and EM parameters.

1. Usual landing at ca. 1e-6 nm for Dmax...OK
2. Last Epot is usually higher than the one before...?
3. Fmax almost monotonically increases...?
4. Not all steps are written, although I'd like to look at them...?
(After MDRUN -using dmxdump and editconf- I put normal atoms
and shell particles in a separate animated XYZ files to see morphing
the input into an output and somtimes miss more details. If it was possible,
I'd take a look also at the Drude optimization steps between two EM steps.)

Setting a_Thole to a different value or rescale too large literature
do not help. In fact, there is no big difference even between applying
or omitting
[thole_polarization] along with [polarization].

One more -for me, now unfortunate- consequence of Thole-ing the
polarizability: after successfully avoiding through-cell bonds in my
PBC simulation, I've now re-introduced them via screening.
Had to set "periodic-molecules = yes" in the MDP file, yet have
the following question.

There are big many A-D particle pairs very close to the walls and,
of course, to other dipoles on the other side.
What if I simply Thole+exclude them like fully internal AD_i-AD_j
pairs of particle pairs? Will it be a long quasi-bond from one wall
to the opposide side-wall or it will just be a short through-wall bond?

I think the majority of the pairs of AD combos are fully inside the
box so I don't expect the full solution from this but it needs be clarified.

You've mentioned correcting the Thole-code by a scale factor.
Can I emulate this correction by scaling the polarizabilities
in the TOP file?


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