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Implementing the Martini Forcefield
- TMichaels
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10 years 6 months ago #2442
by TMichaels
Implementing the Martini Forcefield was created by TMichaels
I wish to implement the MARTIN forcefield, however I am having difficulties finding the equation or source code for the MARTINI forcefield.
I thought that the equation was just a combination of 12-6 LJ and the electrostatic interaction, but I want to make sure.
I also need to know how the parameters in the input files correspond to the equation. For example:
;;;;;; HYDRATED CHLORIDE ION
[moleculetype]
; molname nrexcl
CL- 1
[atoms]
;id type resnr residu atom cgnr charge
1 Qa 1 ION CL- 1 -1.0 1 -1
Where do these parameters fit into the equation?
Also, it seems that I have to use this file as well: md.chem.rug.nl/cgmartini/images/parameters/ITP/martini_v2.0.itp
Where do these parameters fit in?
Thanks
I thought that the equation was just a combination of 12-6 LJ and the electrostatic interaction, but I want to make sure.
I also need to know how the parameters in the input files correspond to the equation. For example:
;;;;;; HYDRATED CHLORIDE ION
[moleculetype]
; molname nrexcl
CL- 1
[atoms]
;id type resnr residu atom cgnr charge
1 Qa 1 ION CL- 1 -1.0 1 -1
Where do these parameters fit into the equation?
Also, it seems that I have to use this file as well: md.chem.rug.nl/cgmartini/images/parameters/ITP/martini_v2.0.itp
Where do these parameters fit in?
Thanks
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- xavier
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10 years 6 months ago #2471
by xavier
Replied by xavier on topic Implementing the Martini Forcefield
You are correct in the type of interactions but you have to consider the switching functions that are applied on both the Coulomb and LJ potentials. There is also a implicit screening of Elec interactions.
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- TMichaels
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10 years 6 months ago #2472
by TMichaels
Replied by TMichaels on topic Implementing the Martini Forcefield
Thankyou. I'm really after a detailed technical description. Source code/algorithm/other technical document.
I've been looking through the list of publications and I have been unable to find such a thing. I have also been unable to locate the source code in GROMACS that describes the MARTINI interaction.
I've been looking through the list of publications and I have been unable to find such a thing. I have also been unable to locate the source code in GROMACS that describes the MARTINI interaction.
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- jaakko
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- Posts: 70
10 years 6 months ago #2474
by jaakko
Replied by jaakko on topic Implementing the Martini Forcefield
Hi,
there is no special Martini interaction, the force field uses just a Lennard Jones and Coulomb interactions with a switch. All these are described in the gromacs manual (switch in section 4.1.5) although you might also want to look at the appendix of dx.doi.org/10.1002/cphc.200600658 due to some apparently still lingering typos in the manual.
there is no special Martini interaction, the force field uses just a Lennard Jones and Coulomb interactions with a switch. All these are described in the gromacs manual (switch in section 4.1.5) although you might also want to look at the appendix of dx.doi.org/10.1002/cphc.200600658 due to some apparently still lingering typos in the manual.
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