[gmx-users] changing simulation length with lambda for TI

David Mobley dmobley at gmail.com
Mon Jul 10 20:18:44 CEST 2006


They are all independent runs, so there is no fundamental reason they
need to be the same length. And in fact you're right -- you'd expect
some simulations to be much slower to converge than others.

Incidentally, are you calculating ion hydration free energies or
something? If so, you might want to see the introduction to the
Lamoureux and Roux hydration free energy paper (J Phys Chem B 2006
110:3308-3322) for some explanation of complications that can arise
concerning hydration free energies of charged species. I am so far
avoiding such things because they make me nervous.


On 7/6/06, Soren Enemark <blegbirk at yahoo.dk> wrote:
>  Dear all,
>  I am wondering if the number of steps in TI simulations need to be the
>  same for all lambda-values. My question comes a situation where I wanted
>  to remove an ion. Once this ion is turned into a dummy atom, it floats
> around
>  and I expect that the phase space to sample becomes much larger, right?
>  On the other hand, when it is captured within a structure the phase space
>  to sample over should be smaller.
>  So, the question is, does it make any sense to increase the simulation
>  length as I am removing the ion?
>  thanks in advance,
>  Søren
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