Re: [gmx-users] How to add iron parameter?

On 10/15/14 2:05 PM, Johnny Lu 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 oribtals? I heard that even calcium is a bit troublesome in

Re: [gmx-users] How to add iron parameter?

"The easiest way" is to simulate QM/MM around Fe (+howmuch?). Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Wed, Oct 15, 2014 at 7:22 PM, Guangyu Zhu 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

Re: [gmx-users] How to add iron parameter?

not sure if this helps. But maillist once mentioned parameter for heme (that are not necessary good): http://comments.gmane.org/gmane.science.biology.gromacs.user/59978 http://ccl.net/chemistry/resources/messages/2008/09/22.001-dir/index.html https://www.mail-archive.com/gmx-users@gromacs.org/msg2

Re: [gmx-users] How to add iron parameter?

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 oribtals? I heard that even calcium is a bit troublesome in md. On Wed, Oct 15, 2014 at 1:22 PM, Gua

[gmx-users] How to add iron parameter?

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 this? [FE] [ atoms] FE FE3.0 [ bonds] [ angles ]