I am completely new to simulation. I need it for my research so I would like to take some suggestions regarding starting simulation from scratch, which softwares to use gromacs or NAMD or anything else, what kind of specifications should the PC have for excecuting simulation. Any suggestion from someone experienced in this field would be appreciated
Trideep Majumdar -- Some molecular dynamics (MD) simulation software is available for all three of the major operating systems (Linux, Mac OS, and Windows). Most MD codes can make use of GPU acceleration using CUDA or sometimes OpenCL. Accordingly, important considertions when choosing a PC for running MD simulations are the specifications of the GPU (video) card(s). In my own experience, I tend to favor running MD simulations on a PC that is running Linux. The specifications of my Linux machine include the following: CPU, AMD TR Pro 5975wx (32 cores/64 threads @ 4.5GHz); 2 x Nvidia A6000 GPUs; 256MB RAM; 2 x 2TB M2.SSDs; 1 x 8TB U2.SSD). I also use a NAS RAID array of HDDs for external storage of MD simulation files. My OS for this machine is Linux Mint 21.3 Xfce. I hope that this information might be helpful to you.
Trideep Majumdar you can try gmx_qk (Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...
). It is made for beginners. If you want to learn it from scratch you can contact me at [email protected].
You can always use amber tutorials in this link: https://ambermd.org/tutorials/.
The good side with those tutorials is, they are being updated when needed, by their authors. I hope this helps and good luck.
Trideep Majumdar As responded by others, Linux is the best OS for scientific computations. You can learn MD from scratch using these tutorial links.
https://www.iitg.ac.in/tamalb/karp/namd/
https://www.ks.uiuc.edu/Training/Tutorials/
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