[gmx-users] How to add iron parameter?
johnny.lu128 at gmail.com
Wed Oct 15 20:45:09 CEST 2014
not sure if this helps. But maillist once mentioned parameter for heme
(that are not necessary good):
On Wed, Oct 15, 2014 at 2:05 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> Pure md doesn't deal with complex orbitals well, I guess. Hydrogen bonds
> in pure md is not directional, as it should be.
> can molecular dynamics (md) simulate heavy metals, like iron, which have d
> I heard that even calcium is a bit troublesome in md.
> On Wed, Oct 15, 2014 at 1:22 PM, Guangyu Zhu <gzhu at hwi.buffalo.edu> wrote:
>> Hi, I’m a beginner of gromacs. I want to do simulation for a protein with
>> protein with ferrous or ferric. But there is no iron in force field. What
>> is easiest way to do it? Can I just add a few lines to aminocids.rtp, like
>> [ atoms]
>> FE FE 3.0000 0
>> [ bonds]
>> [ angles ]
>> [ impropers ]
>> [ dihedrals ]
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