I start to learn the cellulose simulation using Gromacs and NAMD recently, but there are many problems that I haven't figured out yet. I would like to list those questions and some of the solutions that I have learned. Can you give me some suggestions if there is a better way?
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Hey Qing! Using "sudo apt-get install gromacs" is not a good option. It is very easy indeed but it is not good idea. I would suggest you to use the suggestions for the installation of gromacs which are mentioned on their official page for a certain version which you would adopt for your computer architecture by specifying all libraries manually. You shall always know what version you are using because if you will decide to transfer your simulations to a computational cluster they might be not compatible in case if the "default" version on your private machine won't be the same as the one on cluster. Moreover, having more than one version of gromacs on the same machine would be even better. Personally, I am a fan of some routines which exist on older versions.
HI Qing, I am also a beginner in cellulose MD simulations, recently I found a cellulose builder toolkit. Many people have used it for their studies also. However I am stuck at how to use the pdb files generated from it for further simulations. As it uses different force field .Please look into this and try to help
Article Cellulose-Builder: A toolkit for building crystalline struct...
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