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@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
