Hello everyone,
I am trying to see the transportation of iodide and bromide ions from the synthetic ion channel. To run the simulations in NAMD, I need CHARMM force-field for both the ions.
I have been through a paper in which they have used GROMACS MD simulation with SPC/E water type. But I want the parameters calculated using TIP3P water molecule type.
If anyone have idea about it, kindly share it.
Thank you so much in advance.
Do the force field parameters of iodide and bromide ions depend on the water model?
Dear Shruti,
parameters you calculate for an molecule depends on the atoms, bonding patterns and restrains. It is independent of the solvent, you are planning to use. You can use any solvent system, depending upon the level of probability of prediction you wish to achieve, but it comes at the cost of computational time.
regards
Tanuj
Thank you all for replying.
Hi Martin Klvana ,
Yes, force field parameters for any molecule/halide ions (Br-, I-) are depend on the water type.
Here SPC type water has been used to obtain the FF for halide ions : https://www2.icp.uni-stuttgart.de/~mfyta/docs/jcp12.pdf
Wojciech Kopec
, the latest version I could see is 36m in which I could'nt find the parameters.Tanuj Sharma , FF generation is not much tedious, but its validation is.
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