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External Forces and LJ
- panzu
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10 years 5 months ago #2935
by panzu
External Forces and LJ was created by panzu
Hello to everybody,
I was wondering if it were possible to introduce any external local force in gromacs and also if it were possible to change the interaction of LJ from 6-12 to 6-9 for example. It would be interesting..
Thanks in advance,
Sergio
I was wondering if it were possible to introduce any external local force in gromacs and also if it were possible to change the interaction of LJ from 6-12 to 6-9 for example. It would be interesting..
Thanks in advance,
Sergio
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- xavier
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10 years 5 months ago #2936
by xavier
Replied by xavier on topic External Forces and LJ
external local forces: using the pulling code might help … you can apply forces on selected atoms. It all depend on what you want to do.
6-12 -> 6-9: you can implement any potential form using tabulated potentials.
6-12 -> 6-9: you can implement any potential form using tabulated potentials.
panzu wrote: Hello to everybody,
I was wondering if it were possible to introduce any external local force in gromacs and also if it were possible to change the interaction of LJ from 6-12 to 6-9 for example. It would be interesting..
Thanks in advance,
Sergio
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- panzu
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10 years 5 months ago #2945
by panzu
Replied by panzu on topic External Forces and LJ
I do not get what the pulling code is... In fact I want to apply forces in particular places...
About the change of the LJ from 6-12 to 6-9, I know that in martini_v2.X.itp there are the tables of interactions but considering that the interaction is LJ 6-12 but I can not really see how I can decide in that file that I want certain interactions such as LJ 6-9. I don not either know how to create a new file in such a way that gromacs supposes that the LJ is such as 6-9.
About the change of the LJ from 6-12 to 6-9, I know that in martini_v2.X.itp there are the tables of interactions but considering that the interaction is LJ 6-12 but I can not really see how I can decide in that file that I want certain interactions such as LJ 6-9. I don not either know how to create a new file in such a way that gromacs supposes that the LJ is such as 6-9.
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- xavier
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10 years 5 months ago #2951
by xavier
Replied by xavier on topic External Forces and LJ
regarding the pull code you might want to look at the GROMACS manual .. in short it is meant to do free energy calculations by applying forces between different group of atoms.
it is not clear what you mean by switching from 12-6 to 9-6. The 9-6 potentials are not implemented in gromacs so you need to put them in manually. The files that you can give contain the actual potential energy so you can generate it with the analytical form you want: 12-6, 9-6, 1-2, etc ...
To create a file you need to know the potential, the associated parameters if any and generate the values of the potential as a function of distance ... check the manual for more details.
In general these question relate more to GROMACS itself and you would potentially get better answerby posting on the gromacs user list.
it is not clear what you mean by switching from 12-6 to 9-6. The 9-6 potentials are not implemented in gromacs so you need to put them in manually. The files that you can give contain the actual potential energy so you can generate it with the analytical form you want: 12-6, 9-6, 1-2, etc ...
To create a file you need to know the potential, the associated parameters if any and generate the values of the potential as a function of distance ... check the manual for more details.
In general these question relate more to GROMACS itself and you would potentially get better answerby posting on the gromacs user list.
panzu wrote: I do not get what the pulling code is... In fact I want to apply forces in particular places...
About the change of the LJ from 6-12 to 6-9, I know that in martini_v2.X.itp there are the tables of interactions but considering that the interaction is LJ 6-12 but I can not really see how I can decide in that file that I want certain interactions such as LJ 6-9. I don not either know how to create a new file in such a way that gromacs supposes that the LJ is such as 6-9.
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- panzu
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10 years 5 months ago #2952
by panzu
Replied by panzu on topic External Forces and LJ
Thanks Xavier a lot! I will write on GROMACS forum
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