On Thu, Nov 15, 2012 at 4:03 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/15/12 10:55 AM, Steven Neumann wrote: >> >> On Thu, Nov 15, 2012 at 3:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 11/15/12 10:41 AM, Steven Neumann wrote: >>>> >>>> >>>> atomtypes.atp >>>> >>>> FE 55.84700 ; heme iron 56 >>>> >>>> ffnonbonded >>>> >>>> FE 9 18.998 0.000 A 0.115816833358244 -0 >>>> >>>> aminoacids.rtp >>>> >>>> [ FE ] >>>> [ atoms ] >>>> FE FE 2.00 0 >>>> >>>> >>>> Hmmmm, confusing... >>>> >>> >>> What force field is that? None of those parameters seem to come from any >>> of >>> the default force fields in Gromacs. The entry in ffnonbonded is clearly >>> wrong, with the parameters appearing to belong to fluorine rather than >>> iron, >>> but the line appears to have been mangled. It looks most like CHARMM, >>> but >>> someone has messed with ffnonbonded.itp. >>> >>> Regardless, if you look at the parameters for FE in any of the force >>> fields >>> in Gromacs, you will see that their nonbonded parameters (C6/C12 or >>> sigma/epsilon) are generally set to zero. They interact only via ionic >>> interactions because they were likely only intended for use in cofactors >>> like heme, where other bonded parameters fix their geometry. Using them >>> as >>> free ions makes little sense. >>> >>> >>> -Justin >>> >> >> This is charmm27 but modified as you can see. Shall I use: >> >> FE 26 55.84700 2.000 A 0.115816833358 0 >> 0 >> >> in original Gromacs charmm it is >> >> FE 26 55.84700 0.000 A 0.115816833358 0.0 ; >> partial charge def not found >> > > These changes will have no effect and will not solve your problem. The > charge field in ffnonbonded.itp is never used for anything. I don't know > what the extra zero is intended for, but it will probably break the ability > of grompp to read the file. > > Moreover, the point of my previous comments was that your use of this atom > type is not appropriate. The FE atom type still has zero repulsive > interactions, unless explicitly calculated with each atom type. As far as I > can tell from ffnonbonded.itp, this repulsive term is zero for every > interaction, meaning no matter what you do, your Fe ions will always collide > with something negatively charged because there are no LJ terms to impede > the Coulombic attraction, leading to an infinitely negative potential at a > fixed point and thus the crash. > > You need to find better parameters entirely if you wish to simulate free Fe > ions. > > -Justin
Thank you for this. I will try to look at Charmm forum for those parameters. I was also thinking about parameters which Zn(2+) has got as they have similar mass. What do you think? Steven > > > -- > ======================================== > > 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 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 -- 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