[gmx-users] free energy and fatal error
mgoette at mpi-bpc.mpg.de
Tue Jun 27 11:23:49 CEST 2006
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
David Mobley wrote:
>> 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.
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