[gmx-users] free energy and fatal error

[Maik Goette]

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
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> .
>