Soren Enemark 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?
no. just check the whether the dG/dl curve converges, and if so what the
error is.
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?
yes.
thanks in advance,
Søren
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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
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