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

[Justin Lemkul]

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
>>
> 

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================