Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
David Mobley wrote:
Murat,
I am using GROMACS 3.2.1.
I wrote the tutorial you are following. It is for GROMACS 3.3/3.3.1.
If I remember correctly, sc-power is an option that is new to GROMACS
3.3, hence the tutorial will not work in 3.2.1. It is likely that the
"blowing up" you are experiencing is due to using soft core parameters
which are inappropriate.
> I think, it has nothing to do with the error, you experience, but
> delta_lambda should be 1/number of steps, if you want to do TI from
0 to 1.
I follow the solvation FE tutorial by Dill group. These are the
parameters that
they provide
Maik was referring to the time-dependent scheme for changing lambda,
which I don't particularly recommend.
David
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