[gmx-users] RE: VDW parameters: Martini Forcefield + Implicit Solvation
Mark.Abraham at anu.edu.au
Fri Apr 1 04:55:40 CEST 2011
On 1/04/2011 10:57 AM, emendez at ucalgary.ca wrote:
> Thanks for your promt reply Mark.
> Of course I know what is the format, that is implied in my question....
Leaving things to implication is risky. People do misunderstand,
unfortunately. Fault in such cases varies :-) If what you actually want
is gbr and hct parameters for Martini atom types, everyone can use their
time better if you ask specifically about that.
> what I would like to know is if anybody has the specific parameters for
> the amber forcefield. I will try using the gbr parameters from the sigma
> in the LJ potentials, but I am not sure about the proper hct (or the
> other numbers) hence I am inquiring about this,
That manual section mentions the reference sources for these parameters,
which is why I referred to it. Whether there's any established procedure
for implicit solvation with Martini is probably a question for
literature search and speaking with the Martini developers.
> Eduardo Mendez
>> I am trying to do Martini Forcefield + Implicit solvation model for a
>> large system and I need to supply parameters for the
>> [ implicit_genborn_params ]
>> section. Which I have not found.
>> The syntax is
>> Atomtype sar st pi gbr hct
>> Can anybody provide me a clue about where I can find these parameters?
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