simon sham wrote:
Hi,
I have a crystal structure with several SO4 ions.
According to the online manual, the source is ffgmx.rtp. But I could not
find it in
/gromacs/share/top directory. I also could not find it in several force
field files.
You haven't said which Gromacs version you're using, but if it's in the 4.5.x
series, there has been a complete overhaul of force field organization. So
there are no more "ff*.rtp" files; they're all in *.ff subdirectories and called
"aminoacids.rtp" (with a few force fields having lipids.rtp, rna.rtp, and
dna.rtp). For instance:
$ grep -R SO4 */*.rtp
gmx.ff/aminoacids.rtp:[ SO4 ]
gromos43a1.ff/aminoacids.rtp:[ SO42- ]
gromos43a2.ff/aminoacids.rtp:[ SO42- ]
gromos45a3.ff/aminoacids.rtp:[ SO42- ]
gromos53a5.ff/aminoacids.rtp:[ SO42- ]
gromos53a6.ff/aminoacids.rtp:[ SO42- ]
Just curious how people have treated this ion in their simulations.
You're better off not using ffgmx. The manual describes the reasons for this
very clearly. A newer Gromos96 variant might be more suitable, or other
(potentially better) parameters that might exist in the literature.
-Justin
Thanks for your help.
Simon Sham
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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