Soren, 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. David On 7/6/06, Soren Enemark <[EMAIL PROTECTED]> 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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