[gmx-developers] turning charges on/off

[David van der Spoel]

Mark Abraham wrote:
> Jason de Joannis wrote:
> 
>> Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
> 
> 
> I'm keeping the discussion on-list.
> 
>>> Jason de Joannis wrote:
>>>
>>>> I wonder if it is possible to turn charges on and off during the 
>>>> course of a simulation. Will PME still work? (I want to do monte 
>>>> carlo mutations between different molecular species)
>>>
>>>
>>>
>>> So long as your system is well-defined at each time step, why 
>>> wouldn't PME work? That algorithm isn't dependent on previous steps.
>>
>>
>> Well that is good news. I was thinking that there might be some kind 
>> of pme array initializations etc that depend on number of charges.
> 
> 
> :-) The algorithm doesn't, but the implementation might have something 
> like the problem you suggest. I was thinking of higher-order problems!
> 
>>> Anyway, this sort of thing isn't implemented in gromacs, and I 
>>> imagine would be a large amount of work to implement. Good luck!
>>>
>>> Mark
>>>
>> It shouldn't be that much work (hopefully). Just change the q-value 
>> and hopefully Gromacs picks up on that... I will look into it some 
>> more today.
> 
> 
> If it's just a change, then that might be painless, but if you're 
> changing the number of charges, as you imply above, then things might be 
> messy. Better would be to define all the sites originally, and zero the 
> charges for whatever isn't needed at a given step.
> 

Yes, that sounds good. You probably want to define two topologies, an A 
and a B state like in FEP calculations. The you turn off the FEP and
do your algorithm.  Are you planning to implement constant pH simulations?

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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