Hello,
I have seen some papers simulating cellulose in GROMACS software. I have not tried the simulation of non-protein or DNA molecules in GROMACS and want to know how should I use cellulose in my simulaitons using GROMACS since only residues are recognized in this software and from the starting code pdb2gmx residues are the recognized input file for this purpose.
Can anyone help me with this issue of how could I perform MD simulations of cellulose in GROMACS since I have seen some articles with this related topic.
Thanks.
You can easily simulate cellulose in GROMACS, The problem that you are facing is just force fields, you are making topology files using pdb2gmx which is not recognizing the the names you used in your initial .gro/.pdb file. So, for ease, try ATB (https://atb.uq.edu.au/) for generating initial .itp and .top files. The simulations will work properly.
Hi,
Gromacs is a simulation engine, and you can simulate anything given that you have proper parameters and starting configuration. Your cellulose parameters are not by default present in the FF offered by GROMACS. Currently, protein, NA and few non-standard amino acids are supported.
There is a tutorial for protein-ligand complex where Dr. Justin Lemkul has provided a way to conduct simulations for non-standard molecules (in this case the "ligand") and also provided few tools of how to get proper parameters for the ligand. You need to be careful and better to search for already reported parameters.
Here is a link for that tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html
A quick search gave me this thesis regarding your query, you can adopt cellulose parameters from this:
https://pdfs.semanticscholar.org/75d7/f22625206ac015ee838a18e5d4329ec1c65d.pdf
Good luck
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