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Martini in CHARMM
- cicedew
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11 years 1 month ago #1429
by cicedew
Martini in CHARMM was created by cicedew
Does anyone knows how to use Martini in CHARMM?
I am trying to do this, but got one problem in the angle
potential. Martini uses a gromos96 function
0.5*k1*(cos(theta) - cos(theta0))^2
but CHARMM uses a single minimum function as
0.5*k*(theta-theta0)^2.
Anyone ever tried to solve this?
I am trying to do this, but got one problem in the angle
potential. Martini uses a gromos96 function
0.5*k1*(cos(theta) - cos(theta0))^2
but CHARMM uses a single minimum function as
0.5*k*(theta-theta0)^2.
Anyone ever tried to solve this?
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11 years 1 month ago #1434
by xavier
Replied by xavier on topic Martini in CHARMM
Yes this is an issue some people have encounter. They solved the problem by converting the cos(theta) into a regular harmonic angle.
The person doing the conversion was Anu Nagarajan in the laboratory of Tom Woolf. You can look up the have a couple of papers but the final conversion was not tested as I wished it would and they stopped answering my emails. So the use of that conversion is at your own risks ...
The person doing the conversion was Anu Nagarajan in the laboratory of Tom Woolf. You can look up the have a couple of papers but the final conversion was not tested as I wished it would and they stopped answering my emails. So the use of that conversion is at your own risks ...
cicedew wrote: Does anyone knows how to use Martini in CHARMM?
I am trying to do this, but got one problem in the angle
potential. Martini uses a gromos96 function
0.5*k1*(cos(theta) - cos(theta0))^2
but CHARMM uses a single minimum function as
0.5*k*(theta-theta0)^2.
Anyone ever tried to solve this?
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11 years 1 month ago #1451
by cicedew
Replied by cicedew on topic Martini in CHARMM
Looks like CHARMM has the gromos angle potential by setting angle to a negative value in the prm file. Tested on C37a2, not sure about other versions.
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11 years 1 month ago #1454
by xavier
Replied by xavier on topic Martini in CHARMM
mmmmm ... sounds strange. Are you sure about this? How did you find out/test?
Do you know about the implementation I mentioned?
I had a talk with B. Brooks who should know but did not mention that. He mentioned the code should be there but would need to be activated ...
Do you know about the implementation I mentioned?
I had a talk with B. Brooks who should know but did not mention that. He mentioned the code should be there but would need to be activated ...
cicedew wrote: Looks like CHARMM has the gromos angle potential by setting angle to a negative value in the prm file. Tested on C37a2, not sure about other versions.
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11 years 1 month ago #1465
by cicedew
Replied by cicedew on topic Martini in CHARMM
I do not test it throughly, only used a simple residue with one angle. The angle energy given by CHARMM is the gromos energy. Woolf's lab used an approximation, definitely not the best solution.
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11 years 1 month ago #1466
by xavier
Replied by xavier on topic Martini in CHARMM
That is pretty good! That might indicate that they implemented the cos angles in the latest code!
If you come to an implementation of MARTINI into CHARMM and wish to do some testing of it to make sure it is compatible let us know and we would be very happy to give access to the files on the website.
XAvier.
If you come to an implementation of MARTINI into CHARMM and wish to do some testing of it to make sure it is compatible let us know and we would be very happy to give access to the files on the website.
XAvier.
cicedew wrote: I do not test it throughly, only used a simple residue with one angle. The angle energy given by CHARMM is the gromos energy. Woolf's lab used an approximation, definitely not the best solution.
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