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

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 6 20:22:12 CEST 2006

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?


>  thanks in advance,
>  Søren
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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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