Hello Everyone!
I am working on a project of DNA regulation of Nanoenzymes and need to do simulations of nanoenymes. Can anyone tell me how to do MD simulations of inorganic nanoparticles (nanosomes) through GROMACS? I already read some literature about MD simulations of nanoparticles but specifically with GROMACS I couldn't find any literature about simulations.
Your answers will be much appreciated.
Thanks
You may want to start with the tutorials of GROMACS first. They will give you enough perspective.
http://www.mdtutorials.com/gmx/
Ali Khodayari I already working on learning with GROMACS tutorials but i want to know that steps for nanoparticles simulation is same for protein-ligand simulations? like water model etc and input files? If you have any tutorial regarding nanoparticles simulations with GROMACS please share.
it will be very helpful.
thanks
Here I prepare to make a gromacs simulation on gold nanoparticles (I refer the webpage, http://sobereva.com/153) and DNA base cytosine , but when grompp, it prompts the error like this ,
==============================================
ERROR 1 [file topol.top, line 14]: Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr = 3)
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I don't know how to solve. I want to consult google, but I couldn't open google in C-N. here I can only open bing but bing couldn't offer more help for the error. I don't know how to solve. Thank you !
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