[gmx-users] Dissociation of Ligand-reg

[Justin A. Lemkul]

ITHAYARAJA wrote:
> 
> Dear Sir,
> 
> Greeting!
> 
> I convey my thanks to your kind reply for rising whatever doubts and 
> troubles in gromacs.
> 
> I able to do my simulation with desire ligand following your 
> instruction. Now I am interested to simulate the dissociation of bound 
> ligand particularly one molecule among three. Sir, I need your help to 
> do this dynamics study. I also went through some article which refers to 
> SMD, TMD, IMD, REMD and AFM pulling able to do the job. So, Kindly 

Not all of these are applicable.  In general, SMD refers to "steered molecular 
dynamics," or COM pulling.

> instruct me which one can support gromacs for ligand dissociation 
> simulation and What are the parameter set ?
> 

Start with the manual, then have a look at the pertinent tutorial:

http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

If you need further guidance, post a more complete description of what you're 
trying to do, what's in your system, etc.  Anything at this point would be idle 
speculation.  There are no generic pull settings that will necessarily work for 
any system.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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