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

[Hermann, Johannes]

Thank you very much, Justin!

Best

Johannes


On 06.07.2017 14:43, Justin Lemkul wrote:
>
>
> On 7/6/17 8:42 AM, Hermann, Johannes wrote:
>> 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.
>>
>
> Yes, because it was important to correct the record and because 
> failing to change the subject and replying to the whole digest is 
> incorrect list etiquette.
>
>> 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 before...
>>
>
> Your approach is fine.
>
> -Justin
>
>> I will highly appreciate it!
>>
>> Thanks!
>>
>> Johannes
>>
>> -----------------------
>>
>> 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
>> Johannes
>>
>> -----------------------
>>
>> 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
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de
http://www.biovt.mw.tum.de/