On 11/15/12 10:26 AM, Steven Neumann wrote:
I tried both options and now different atom is responsible of this
(Oxygen from small molecule next to Fe). With nstxout = 1 I observed
the trajectory -> My Fe(2+) is coming very close to the Oxygen atom
and it looks that their coordinate became equal: in VMD Oxygen absorbs
Fe(2+) and the atom disappears :) Any suggestions?
It sounds like the Fe-O interaction is insufficiently repulsive. What
parameters are you using for the Fe? These ions (and transition metals in
general) are usually very poorly described by most MD force fields.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
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 [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
