- Posts: 5
Martini in CHARMM
- cicedew
- Topic Author
- Offline
- Fresh Boarder
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?
Please Log in or Create an account to join the conversation.
- xavier
- Offline
- Admin
- Posts: 416
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?
Please Log in or Create an account to join the conversation.
- cicedew
- Topic Author
- Offline
- Fresh Boarder
- Posts: 5
Please Log in or Create an account to join the conversation.
- xavier
- Offline
- Admin
- Posts: 416
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.
Please Log in or Create an account to join the conversation.
- cicedew
- Topic Author
- Offline
- Fresh Boarder
- Posts: 5
Please Log in or Create an account to join the conversation.
- xavier
- Offline
- Admin
- Posts: 416
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.
Please Log in or Create an account to join the conversation.