[CP2K-user] [CP2K:18361] Re: Guided AIMD reaction, CONSTRAINT, RESTRAINT, METADYNAMICS
Dobromir A Kalchevski
dobromirak at gmail.com
Fri Jan 20 14:00:59 UTC 2023
This is the colvar:
&COLVAR
&DISTANCE
AXIS XYZ !DEF XYZ, ANY COMBINATION
ATOMS 50 81
&END DISTANCE
&END COLVAR
and with restraint it moves the C atom from methane (reacting molecule) to
a Si atom in the Si lattice, the way it's supposed to, it just goes too far.
Best Regards,
Dobromir
On Friday, January 20, 2023 at 3:32:09 PM UTC+2 Marcella Iannuzzi wrote:
>
> Most probably you defined the COLVAR in the wrong way.
> If there is an activation barrier in this reaction, this will never happen
> in the right way just crashing the molecule into the surface
>
> Regards
> Marcella
>
>
> On Friday, January 20, 2023 at 2:14:26 PM UTC+1 Dobromir A Kalchevski
> wrote:
>
>> Still, my supervisor doesn't want me to study the FES, he simply wants me
>> to make the reaction happen in dynamics. He wants the molecules to move
>> around and eventually a reaction to occur.
>>
>> Even if I try
>>
>> &CONSTRAINT
>> &COLLECTIVE
>> COLVAR 2
>> INTERMOLECULAR
>> TARGET [angstrom] 5.0
>> !initial position in the xyz geometry file
>> TARGET_GROWTH [angstrom*fs^-1] 0.01
>> TARGET_LIMIT [angstrom] 2.0
>> &END COLLECTIVE
>> &END CONSTRAINT
>>
>> cp2k drives the two atoms from the COLVAR to a distance of 2.0 angstrom
>> IMMEDIATELY. Is this normal or is it a bug ?
>>
>> And once again, why does RESTAINT with 1 kcal/mol K drive the molecule
>> into the surface lattice, pushing lattice atoms around and integrating the
>> C atom from the methane into the lattice ? Could it be due to DFTB
>> parameterization or is it a bug or am I missing something ?
>>
>> Best Regards,
>> Dobromir
>> On Friday, January 20, 2023 at 2:35:31 PM UTC+2 Dobromir A Kalchevski
>> wrote:
>>
>>> Dear Marcella Iannuzzi,
>>>
>>> Thank you for your reply.
>>>
>>> Best Regards,
>>> Dobromir
>>>
>>> On Friday, January 20, 2023 at 2:21:37 PM UTC+2 Marcella Iannuzzi wrote:
>>>
>>>> Dear Dobromir
>>>>
>>>> The TARGET is the initial value that is imposed to the variable, as it
>>>> is defined.
>>>> The TARGET_GROWTH is the rate of change of that target value, which in
>>>> the example you posted is ridiculously high:
>>>>
>>>> TARGET_GROWTH {Real}
>>>> *Specifies the growth speed of the target value of the constrained
>>>> collective variable.*
>>>>
>>>> The constraint with the value determined by the growth rate will be
>>>> imposed, no matter which are the other forces in place.
>>>> At least until the calculation does not converge anymore and everything
>>>> explodes.
>>>>
>>>> Nothing of this is a sampling in the NVT ensemble, anyway.
>>>>
>>>> If the goal is to sample the final state after the reaction has
>>>> occurred, just start a simulation from the configuration of the reacted
>>>> molecule.
>>>> If the goal is to find the reaction mechanism, there is no way out of
>>>> studying the free energy surface or, in simpler cases, the potential energy
>>>> surface.
>>>> An efficient way to find the potential minimal energy pathway in
>>>> cases like yours is in general the nudged elastic band approach.
>>>>
>>>> Regards
>>>> Marcella
>>>>
>>>>
>>>> On Thursday, January 19, 2023 at 9:42:15 PM UTC+1 Dobromir A Kalchevski
>>>> wrote:
>>>>
>>>>> Hello everyone!
>>>>>
>>>>> I want to make a molecule occasionally approach a surface and react
>>>>> with it in a NVT ensemble production run. I don't want it fixed in
>>>>> predetermined coordinates and I don't want it to fly away or to wait for
>>>>> too long of a trajectory.
>>>>> For now I don't want to study the reaction's thermodynamics.
>>>>> Experimentally the reaction occurs.
>>>>>
>>>>> I tried the following approaches without success:
>>>>>
>>>>> I defined a COLVAR for the distance between one surface atom (Si) and
>>>>> the center atom (C) of the gas phase reagent molecule (methane)
>>>>>
>>>>> &COLVAR
>>>>> &DISTANCE
>>>>> AXIS XYZ !DEF XYZ, ANY COMBINATION
>>>>> ATOMS 50 81
>>>>> &END DISTANCE
>>>>> &END COLVAR
>>>>>
>>>>> and then I defined a CONSTRAINT
>>>>>
>>>>> &CONSTRAINT
>>>>> &COLLECTIVE
>>>>> COLVAR 2
>>>>> INTERMOLECULAR
>>>>> TARGET [angstrom] 1.87
>>>>> TARGET_GROWTH [angstrom*fs^-1] 0.25
>>>>> TARGET_LIMIT [angstrom] 5.0
>>>>> &END COLLECTIVE
>>>>> &END CONSTRAINT
>>>>>
>>>>> The result is that both atoms get closer too quickly and the system
>>>>> gets an unphysical geometry - the Si kind of moves too far away from it's
>>>>> lattice and the C abandons its hydrogens. The remperature rises too quickly
>>>>> to unbelievable degrees, the calculation slows down and eventually the
>>>>> program dies.
>>>>> My cell is defined just fine, with enough space for the gas reagent to
>>>>> move around. I use a XYZ PBC with space left in one dimension so it
>>>>> effectively becomes 2D. In that space is the reacting molecule.
>>>>> I tried playing with TARGET_GROWTH with many values from 0.01 to 5.0
>>>>> and the result is always the same.
>>>>> In this group I read that the moment TARGET is set the atoms are also
>>>>> set at that distance, so I tried switching TARGET and TARGET_LIMIT, but
>>>>> even then the result is the same - wrong geometry, they get too close too
>>>>> quickly even with very low TARGET_GROWTH, too high temperature - program
>>>>> dies.
>>>>> - Is this a bug, because it makes no sense as expected behavior ?
>>>>>
>>>>> I also tried using a RESTRAINT:
>>>>>
>>>>> &CONSTRAINT
>>>>> &COLLECTIVE
>>>>> COLVAR 2
>>>>> INTERMOLECULAR
>>>>> TARGET [angstrom] 3.0
>>>>> &RESTRAINT
>>>>> K [kcalmol] 1.0
>>>>> &END RESTRAINT
>>>>> &END COLLECTIVE
>>>>> &END CONSTRAINT
>>>>>
>>>>> with the COLVAR being a plane between 3 surface atoms:
>>>>>
>>>>> &COLVAR
>>>>> &DISTANCE_POINT_PLANE
>>>>> &POINT
>>>>> TYPE GEO_CENTER
>>>>> ATOMS 8
>>>>> &END POINT
>>>>> &POINT
>>>>> TYPE GEO_CENTER
>>>>> ATOMS 21
>>>>> &END POINT
>>>>> &POINT
>>>>> TYPE GEO_CENTER
>>>>> ATOMS 28
>>>>> &END POINT
>>>>> &POINT
>>>>> TYPE GEO_CENTER
>>>>> ATOMS 81
>>>>> &END POINT
>>>>> ATOMS_PLANE 1 2 3
>>>>> ATOM_POINT 4
>>>>> &END DISTANCE_POINT_PLANE
>>>>> &END COLVAR
>>>>>
>>>>> and the gas phase reagent does not stop at the TARGET distance,
>>>>> instead it gets inserted into the Si lattice, pushing Si atoms away,
>>>>> inserting both C and H from the methane and one of the hydrogens flied far
>>>>> away. Temperature goes anomalously high, program slows down, dies. At least
>>>>> it took some time and steps to get to the wrong point.
>>>>> - Why didn't the molecule stop at the surface, while experiencing the
>>>>> forces of the lattice atoms ?
>>>>> - Why did it do beyond the TARGET distance ?
>>>>> - Is this a bug ?
>>>>>
>>>>> Can I use metadynamics in any way to push the molecule towards the
>>>>> surface for a reaction to occur ? Once again, I'm not interested in
>>>>> studying the FES or the rest of the thermodynamics.
>>>>>
>>>>> I just need a way to get the gas phase reagent to occasionally get
>>>>> close enough for a reaction.
>>>>>
>>>>> I think the answers to those question can be very useful for many.
>>>>>
>>>>> I attach some pictures of the anomalous results. The first two are
>>>>> from the CONSTRAINT, the 3rd is from the RESTRAINT.
>>>>>
>>>>> Best Regards,
>>>>> Dobromir
>>>>>
>>>>
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