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Tabulated potential
- lsamba
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7 years 8 months ago #5798
by lsamba
Tabulated potential was created by lsamba
I am working on GROMACS and I am mapping a surfactant molecule to coarse grain bead. I did that successfully. My question is that the bonded interaction between those beads will be considered as a bonded interaction as it is in a covalent bond or the beads will be non bonded? I am generating tabulated potentials. Are these tabulated potentials a kind of bonded potential? If not then how are they different from Lennard Jones potential?
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- peterkroon
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7 years 7 months ago - 7 years 7 months ago #5806
by peterkroon
Replied by peterkroon on topic Tabulated potential
Ok, let's see.
There's a bond between two beads iff any atom in bead 1 is bonded to any atom bead 2. All bonds will result in bonded interactions.
You can use tabulated potentials for any interaction (bonds, angles, dihedrals, non-bonded, ...). You probably do not want to use tabulated potentials for your non-bonded interactions, since those potentials come from the Martini forcefield. You're free to use them for bonded interactions.
"Tabulated potentials" is a term that says that rather than evaluating some analytical function (such as LJ, or harmonic) you look up the value for the potential in a table.
HTH!
There's a bond between two beads iff any atom in bead 1 is bonded to any atom bead 2. All bonds will result in bonded interactions.
You can use tabulated potentials for any interaction (bonds, angles, dihedrals, non-bonded, ...). You probably do not want to use tabulated potentials for your non-bonded interactions, since those potentials come from the Martini forcefield. You're free to use them for bonded interactions.
"Tabulated potentials" is a term that says that rather than evaluating some analytical function (such as LJ, or harmonic) you look up the value for the potential in a table.
HTH!
Last edit: 7 years 7 months ago by peterkroon.
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- xavier
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7 years 7 months ago #5835
by xavier
Replied by xavier on topic Tabulated potential
If I understand correctly, you wonder if using a tabulated potential for bonded terms will be counted as regular bonded term and thus exclude the beads from non-bonded lists.
This depends on how you define the use of tabulated potentials. You need to go in the Gromas manual at the definition of the bonded terms and check how the tabulated type you use removes the non-bonded terms or not. In the grimace-2016 pdf manual the info is in Table 5.5 page 137-9.
Note that in Martini beads connected with bond-angles and dihedral-angles are not automatically excluded.
This depends on how you define the use of tabulated potentials. You need to go in the Gromas manual at the definition of the bonded terms and check how the tabulated type you use removes the non-bonded terms or not. In the grimace-2016 pdf manual the info is in Table 5.5 page 137-9.
Note that in Martini beads connected with bond-angles and dihedral-angles are not automatically excluded.
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