Dear Tamas,
Just a small note on the subject.
Keep in mind that particular choice of atom and shell values (while q_A+q_D
remains constant) may influence some properties of the system. More details can
be found in Asmadi at al. (Journal of Molecular Liquids 188 (2013) 245-251).
Although, for
On 8/1/14, 6:13 AM, Tamas Karpati wrote:
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
Dear Justin,
I'm in the experimenting with [exclusions] for [thole_polarization].
Still not there but approaching... I'd like to ask more help as the
Manual is not detailed enough for me to comprehend the whole.
When using the core/shell model I expect the following extra
effects and functions
Dear Justin,
1. With a q_D charge on D, the normal q_A becomes q_C=q_A-q_D
to preserve the q_A=q_C+q_D atomic charge in a c/s simulation
(since D is attached to A). I assume that GROMPP expects q_C for
atoms, q_D for shell particles in the GRO files. Is this correct?
No. Every atom in
On 7/31/14, 2:17 PM, Tamas Karpati wrote:
Dear Justin,
1. With a q_D charge on D, the normal q_A becomes q_C=q_A-q_D
to preserve the q_A=q_C+q_D atomic charge in a c/s simulation
(since D is attached to A). I assume that GROMPP expects q_C for
atoms, q_D for shell particles in the GRO
Dear Justin,
No, they're not mutually exclusive. The Thole function screens nearby
dipoles so they don't experience artificial forces. The
thole_polarization name is a bit unfortunate; it should really be
thole_screening instead.
I was probably confused by the two contribs in the MDRUN log
On 7/30/14, 5:14 AM, Tamas Karpati wrote:
Dear Justin,
No, they're not mutually exclusive. The Thole function screens nearby
dipoles so they don't experience artificial forces. The
thole_polarization name is a bit unfortunate; it should really be
thole_screening instead.
I was probably
On 7/30/14, 9:37 AM, Tamas Karpati wrote:
But in short, no, bonds are not compulsory for using Thole, but exclusions
definitely are. I would exclude at least the nearest-neighbor interactions.
Does this mean that by [thole_polarization] I define bonded interactions
which can be dropped by
Dear Justin,
I've tried applying the [thole_polarization] section in
the format you've suggested. I've noticed the followings.
1. First I made a mistake and forgot to remove the [polarization]
section from the TOP file. Even this way MDRUN worked and indicated
the usual ca. 10 kJ/mol
On 7/29/14, 9:33 AM, Tamas Karpati wrote:
Dear Justin,
I've tried applying the [thole_polarization] section in
the format you've suggested. I've noticed the followings.
1. First I made a mistake and forgot to remove the [polarization]
section from the TOP file. Even this way MDRUN worked
Dear all,
I have two questions about geometry optimization of a crystal
with polarization via the core/shell model. I'm creating *.gro and
*.top files by hand and compile them with *.mdp to *.tpr via
GROMPP. My FF is also made by hand (simply because i need
to learn GROMACS). I have learnt on
On 7/25/14, 7:43 AM, Tamas Karpati wrote:
Dear all,
I have two questions about geometry optimization of a crystal
with polarization via the core/shell model. I'm creating *.gro and
*.top files by hand and compile them with *.mdp to *.tpr via
GROMPP. My FF is also made by hand (simply because
Dear Justin,
Thank you for your quick answer.
Same with GROMACS-4.6.6: core-to-shell distance
must be 0 to not crash. My crystal is expected to be polarized
(metallic and oxygen sites are the victims of this model).
The *.mpd file being used is:
# nstcalcenergy = 1 ; 4.6.6 claims this
On 7/25/14, 8:10 AM, Tamas Karpati wrote:
Dear Justin,
Thank you for your quick answer.
Same with GROMACS-4.6.6: core-to-shell distance
must be 0 to not crash. My crystal is expected to be polarized
Does your topology specify the proper intramolecular exclusions? What is(are)
the
On 7/25/14, 11:22 AM, Tamas Karpati wrote:
Dear Justin,
Does your topology specify the proper intramolecular exclusions? What
is(are) the molecule(s)?
No bonds, no exclusions. The whole crystal is modelled by ions
interacting via forces of the Coulomb and Buckingham types.
In fact, there
Dear Justin,
Does your topology specify the proper intramolecular exclusions? What
is(are) the molecule(s)?
No bonds, no exclusions. The whole crystal is modelled by ions
interacting via forces of the Coulomb and Buckingham types.
In fact, there is an X-Y-X angle force type which does have an
Dear Justin,
Thanks for your educational answers.
Coulombic interactions fail at short distances; you probably need to apply
I was afraid of that... somehow removing shells from the cores in the
initial structure have let it functionally work (with not yet
reasonable results).
Thole
On 7/25/14, 12:40 PM, Tamas Karpati wrote:
Dear Justin,
Thanks for your educational answers.
Coulombic interactions fail at short distances; you probably need to apply
I was afraid of that... somehow removing shells from the cores in the
initial structure have let it functionally work
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