Good evening Dr. Simmering.
First of all, thanks for your prompt answer, and sorry for my delayed response.
It took me a while to get the openff nomenclature (maybe there are still points I'm not getting exactly, but the picture is much clearer now), but I got that the second openff version (sage) is the one to look for in terms os LJ parametrization.
Moreover, it is still a bit similar to the old days original opls LJ parametrization: simulate liquids and adjust densities and enthalpies. Biggest difference is the clever introduction os mixtures properties (at the price of less atom types being available for parametrization: it might prove or not yo be useful for me further down this road) instead of pure liquids.
*However*, it still called my attention is that they used ForceBalance on their procedures. While clearly it is done with several accessory programs, when I studied the original ForceBalance paper it seemed to rely on (one molecule of) "water dissolved solutes" to optimize the bonded interaction (given that it does not seems to evaluate LJ) potencial parameters. I've found it strange, but also understood that as a huge move away from more traditional optimization, specially dihedrals, as seen for example in Paramfit
So, what is really the differences between Paramfit and ForceBalance? Can I do the same "traditional" parametrization of Paramfit within ForceBalance? Do I need to have water solutions simulated in ForceBalance, or can I deal with mixtures and/or pure liquids? ForceBalance can or cannot optimize LJ parameters by itself?
Thanks a lot in advance for any help provided.
Best regards,
Jones
Em 19 de setembro de 2024 15:54:57 BRT, Carlos Simmerling via AMBER <amber.ambermd.org> escreveu:
>you might check into what the openFF group is doing and see if they have
>any tools, there models tend to be Amber-compatible in terms of functional
>form.
>
>On Thu, Sep 19, 2024 at 2:51 PM Jones De Andrade via AMBER <
>amber.ambermd.org> wrote:
>
>> Hi Dr. Case, thanks for the answer.
>>
>> > You could, of course, define new atom types. But I don't know of any
>> > automated way to do this. Others on the list may have more
>> > information.
>>
>> That is what I'm interested in (sorry if I was not clear in the previous
>> email), define new atoms types, in some cases for different elements.
>>
>> I kinda remember that old VDW parameters were adjusted to fit density
>> and vaporization enthalpies from MC simulations, but I'm not quite sure
>> if it would still be an up-to-date method, neither if someone has ever
>> automatized this or any other approach (I thought that ForceBalance
>> would be able to try to parametrize those too: am I wrong?)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 01 2024 - 15:30:02 PDT
