[gmx-users] Adding FE2+ or FE3+ into the system

[CROUZY Serge 119222]

I'm interested as well in knowing how to get decent parameters for Fe2+

>From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
We have Zn2+  (What is a reference for these parameters ?)

name   bondtype   mass   charge   ptype     C                A
;name  at.num   mass      charge  ptype       c6           c12
ZN2+   30      0.000      0.000     A  0.0004182025  9.4400656e-09

>From which I deduced
if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6
to be compared to the standard V=4*eps*[(sig/r)^12 - (sig/r)^6]
A =4*eps*sig^12
C=4*eps*sig^6
sig = (A/C)^1/6
eps=C^2 / (4 A)
For Zn sig=0.168112  eps=4.631677 kJ/mol

But no Fe2+

Regards

Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux 
Institut de Biosciences et Biotechnologies de Grenoble
CEA Grenoble  UMR  CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K  pièce 110   
Tel (33)0438782963
Fax (33)0438785487
http://big.cea.fr/drf/big/CBM/GMCT



-----Message d'origine-----
De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] De la part de liming_52
Envoyé : mardi 10 janvier 2017 16:54
À : gmx-users at gromacs.org
Objet : [gmx-users] Adding FE2+ or FE3+ into the system

Dear gromacs users,

I want to compare the protein in the buffers with FE2+ and FE3+, respectively. 

How can I add FE2+ or FE3+ into the system? What is the command?

Thanks in advance.





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China
-- 
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.