unanswered Modeling Urea Molecule

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3 months 3 weeks ago #9523 by shalinijr
Modeling Urea Molecule was created by shalinijr
Hi all,

I am trying to model a bulk Urea solvent system with Martini 3 parameters. Urea is modeled as a 3-bead system: U-SP2Dq-U where SP2dq has a charge of 0.0 and the two U beads are non-interacting (LJ) and have charges of +0.35 and -0.35 respectively. The topology as given below consists of length constraints (SP2dq-U) and angle (U-SP2dq-U) to maintain linearity. After a few steps of NVT, the U atoms try to collapse into each other due to electrostatics and LINCS fails. Has anybody run into this issue with Urea or modeling other dipoles and could recommend a way to define constraints/restraints while modeling these type of systems?

Topology (constructed based on the SI in reference (Vainikka et al. CS Sustainable Chem. Eng. 2021, 9, 51, 17338–17350)

[moleculetype]
; molname nrexcl
Urea 1

[atoms]
; id type resnr residu atom cgnr charge
1 SP2dq 1 Urea SP2 1 0
2 U1 1 Urea U1 2 0.35
3 U2 1 Urea U2 2 -0.35

[constraints]
; i j funct length
1 2 1 0.140
1 3 1 0.140

[angles]
; i j k funct angle force.c.
2 1 3 2 0.0 5.0


Thanks,

Shalini

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