[gmx-users] Charge Mutation (State B) for Ions

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Thu Jul 6 14:42:12 CEST 2017

Dear Justin,

I think you were referring to amitabhjayaswal at gmail.com Mails, right? 
You posted the link as answer to his question but now my object is in 
the object line.

However, I am still looking for an answer to my question.

Is there anyone, who can tell me something about my dual topology of my 
MG ions or point me to some literature? I really did my google search 

I will highly appreciate it!




This was my orginal message:

Dear all,

I am doing a FEC via alchemical transformation. In order to keep the 
charge constant I plan to mutate ions at the same time. In particular, I 
want to change the charge of MG ions. My question is did I manipulate 
the .top .itp and .gro file in the right way:

In the topology.top file I added:

#include "topol_MG_Hybrid.itp"

in the beginning and included in the [molecules] section

MG_HBRID            26

at the place where my hybrid MGs begin in the .gro file. In the .tip 
file I defined the new moleculetype and the atom:

[ moleculetype ]
; Name            nrexcl
MG_HBRID                 1
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge mass typeB    
chargeB      massB
    1           MG    1    MGX    MGHBR      1          2 24.305 
MG       2.30769          24.305

In the gro file I changed the (formaly regular) MGs to:

8702MGX  MGHBR55183  -1.480   0.077   2.991

I.e. I changed the residue name to MGX and the atom name to MGHBR. I ran 
grompp and it compiles without errors. However, I want to make sure, 
that this is consistent with gromacs files and that I will change the 
charge in the simulation.

Thank you very much for your help!

All the best


On 06.07.2017 14:24, Justin Lemkul wrote:
> On 7/6/17 12:56 AM, amitabh jayaswal wrote:
>> ... well, this URL under ans.2 (http://www.bevanlab.biochem.
>> vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what 
>> I'm
>> repeatedly getting.
>> Please rectify/improve.
> Because you haven't copied the whole URL, which is split across two 
> lines in that message.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html 
> -Justin

*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
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Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de

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