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Modeling Urea Molecule
- shalinijr
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1 year 6 months 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
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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- LiguoWang
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11 months 2 weeks ago #9629
by LiguoWang
Replied by LiguoWang on topic Modeling Urea Molecule
The reason should be Angle setting, which should be 180 to keep linearity not 0.
The most recent itp of Urea is here: github.com/P-Vainikka/martini3-DES-model...b/main/itps/urea.itp
The most recent itp of Urea is here: github.com/P-Vainikka/martini3-DES-model...b/main/itps/urea.itp
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