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