[gmx-users] Charge Mutation (State B) for Ions
J.Hermann at lrz.tu-muenchen.de
Thu Jul 6 14:42:12 CEST 2017
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:
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:
in the beginning and included in the [molecules] section
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
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
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
>> repeatedly getting.
>> Please rectify/improve.
> Because you haven't copied the whole URL, which is split across two
> lines in that message.
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Tel: +49 8928915730
Fax: +49 8928915714
Email: j.hermann at lrz.tum.de
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