[gmx-users] RE: VDW parameters: Martini Forcefield + Implicit Solvation

[Mark Abraham]

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.

Mark

> Cheers.
>
> Eduardo Mendez
>
>> Greetings,
>>
>> 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?
>
>