Author Topic: Flexible and chiral molecules  (Read 298 times)

bz475

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Flexible and chiral molecules
« on: December 18, 2020, 07:31:13 PM »
Hello everyone,

I am trying to use flexible molecule models and simulate the adsorption process of these molecules into a MOF. Then I have this error message:
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Error: no energy conservation in internal MC scheme (Bend 121.689515)The parameter following 'Bend' changes in every simulation.

The component section in my .input file looks like this:
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Component 0 MoleculeName                  ibuprofen_flex_try
            MoleculeDefinition            local
            StartingBead                  2
            IdealRosenbluthValue          1.0
            WidomProbability              1.0
            CreateNumberOfMolecules       0
            Intra14VDWScalingValue        0.5
            Intra14ChargeChargeScalingValue   0.5

I defined a chiral center in my .def file because ibuprofen is a chiral molecule:
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# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
               1    33            0    58           0      0        80           7         0            0         0               0            0         0            0
# chiral center
5 10 12 11 L
It seems that only four atoms can be read, including the chiral center. Then how do I decide the combination and the sequence of these atoms?

I set the ibuprofen group as rigid accidentally but I don't have the error and the simulation runs perfectly. Does that make sense? Does anyone know how to fix it? Thank you.

David Dubbeldam

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Re: Flexible and chiral molecules
« Reply #1 on: December 23, 2020, 07:38:15 PM »
Did you define a flexible-ring? (RASPA can not handle flexible rings).

bz475

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Re: Flexible and chiral molecules
« Reply #2 on: January 20, 2021, 05:54:35 PM »
Yes. There is a flexible ring in the molecule. I used a rigid/flexible model instead (the ring is fixed; the rest segments are flexible). Then the simulation went well! Thank you for your help.