Hi,
I'm still a bit confused about the [ pairs ] and [ exclusions ] sections
of an .itp file. How would the procedure be if I want to change the
Lennard-Jones parameters for certain pairs of atoms in a molecule? The
reason I ask is that I have created a trehalose topology based on the
56A_CARBO (Hansen & Hünenberger, 2011) parameters, but I'm a bit unsure
that I got the special 1-5 and and 1-4 pair right. This is how I did it
(the modified forcefield is G53A6 or G54A7):
1. Excluded the pairs by putting them in the [ exclusions ] section
2. Added the excluded pairs in the [ pairs ] section with function type
1 followed by the C6 and C12 parameters.
Something like this:
[ exclusions ]
1 5
[ pairs ]
; ft C6 C12
1 5 1 0.22617E-02 0.74158E-06
Is the choice of function right? In the manual it looks like I could
also use function type 3 here. What is more correct?
Regards
Jon Kapla
--
_____________________________________________________
Jon Kapla
Division of Physical Chemistry
Dpt. of Materials and Environmental Chemistry (MMK)
Arrhenius Laboratory
Stockholm University
SE-106 91 Stockholm
Pos: PhD Student
Phone: +46 8 16 11 79 (office)
Phone: +46 70 304 19 89 (cell)
E-mail: jon.ka...@mmk.su.se
_____________________________________________________
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
