[Fwd: Re: [gmx-users] QMMM free energy]

[Gerrit Groenhof]

Hi Fiske,

 From what I understand, you want to compute the free energy for 
changing one or more atoms in the QM subsystem. I never considered doing 
this because I do not expect to get sufficient sampling. But in my 
opinion this should be possible.

In case only atoms in the QM subsystem change it is straightforward. But 
I might overlook something important (maybe someone can comment on this 
if I make a mistake).

I think you should modify the code, so that there are two QM/MM 
computations per step. Once in the A state and once in the B state, 
which gives VA and VB. From that you can compute
V(lambda) = lamda VB + (1-lambda) VA. And dv/dl = VB-VA. This is then 
the QM and coulombic QM/MM contribution to dv/dlambda. The lennerd jones 
should work automatically.

But this works only if you are not modifying the charges of the MM 
atoms. Then things get more messy.

However, there is a problem with neighbour searching. Right now, the 
QM/MM neighbour list is constructed only in the
if (!bFreeEnergy)
branch of the put_in_list function. I think this is why mdrun crashes. 
the qmmm interface expects to find MM neighbours, but the QMMM nblists 
are not created.
You can copy the if(bQMMM) branch into the free energy branch.

Best,

Gerrit





>
> Subject:
> Re: [gmx-users] QMMM free energy
> From:
> Erik Lindahl <lindahl at cbr.su.se>
> Date:
> Wed, 30 May 2007 17:34:59 +0200
> To:
> Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> To:
> Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>
> Hi,
>
> I'm not a QM expert myself (Gerrit, comments?),  but I'm pretty sure 
> the main reason is that you cannot either mutate atom types or 
> decouple interactions gradually in the QM part of the system. Once 
> this is solved for a pure QM system it should be straightforward to 
> implement the QM/MM interface of it.
>
> Cheers,
>
> Erik
>
> On May 30, 2007, at 5:30 PM, Robert fiske wrote:
>
>>> With the original QM/MM implementation, free energy is currently not 
>>> possible (yet). From what you report, I guess that also with the 
>>> CPMD interface it does not work.
>>
>> The CPMD interface is mostly plugged into the same setup as the other 
>> QM interfaces, I was able to bypass the error by copying modifying 
>> the free energy else statement to bypass the vdw calculations for the 
>> case of bQMMM true (and generally try to have that code match the 
>> bQMMM case of non free energy runs).  But since my background is 
>> Computer Engineering and not chemistry (Chemistry 101 is as far as I 
>> got in formal training)  I don't really know what should be done (I 
>> assume since as you said it's not implemented yet although I don't 
>> get a run time error that the results will be off).
>>
>> Are QM/MM free energy calculations substantially different than MM 
>> calculations, or is it just not implemented because no one has needed 
>> to do QM/MM with free energy yet?
>>
>>
>> fiske
>> Gogonea Group
>> Cleveland State University
>>
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> ------------------------------------------------------------------------
>
> Subject:
> Re: [gmx-users] QMMM free energy
> From:
> "Robert fiske" <rfiske_ at hotmail.com>
> Date:
> Wed, 30 May 2007 12:00:29 -0400
> To:
> gmx-users at gromacs.org
>
> To:
> gmx-users at gromacs.org
>
>
>
>> I'm not a QM expert myself (Gerrit, comments?),  but I'm pretty sure  
>> the main reason is that you cannot either mutate atom types or  
>> decouple interactions gradually in the QM part of the system. Once  
>> this is solved for a pure QM system it should be straightforward to  
>> implement the QM/MM interface of it.
>
> One of the main things we plan to do with the free energy code (once I 
> can confirm I'm doing things right) is to modify the charge of the 
> quantum system for the lambda values, so atom types don't need to be 
> modified for this I believe, although I see how that could complicate 
> other types of free energy calculations.  As for decoupling 
> interactions I don't know what impact that has for changing of charge.
>
> For now, are there any major complications if all we want to do is 
> modify the charge from state A to state B (assuming the interaction 
> problems you mentioned aren't a problem)
>
>
> fiske
>
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