[gmx-developers] turning charges on/off
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 20 18:44:11 CEST 2006
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!
>> 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 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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