[gmx-users] RE : FEP : separating components of dgdl

[Maik Goette]

I think, there are some "best" parameters :)
Ich tested them with some smaller systems and found, that sigma=0.3 and 
alpha=0.25 seem to perform quite well.

Regards

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/


BON Michael wrote:
> Hi,
> 
> You were right for the bonds, I forgot that I was using constraints = all-bonds.
> 
> Could the missing term be the soft core then ? Or is it included in VdW ?
> 
> Anyway, I noticed that this problem of hidden extra term happens when I modify something else than a hydrogen. Does it make sense ?
> For example, I did N->DUM with all the parameters kept the same : every components of dVdl are 0 (VdW, Coulomb, angle, proper dihedral, Ryck.,  LJ 1-4, position restraint, disp. corr. ), but dVdl/dlambda is -6. Any idea ?
> 
> Other question : is there some information available about the "best" settings of soft core parameters with amber99 ?
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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