They are both equally good, and widespread in the literature. Go for the one that you have more familiarity with. I personally use GROMACS, since I found the setup, commands and documentation are a bit better, however, there is also good ones in NAMD. Also, NAMD has a plugin to VMD, to make it easier to use (at least for some uses).
https://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server
you can register in the Grid through Supreme Council of Universities-Egypt
Hi,
Here is a comparison of both softwares, though it is old but will give you an insight:
https://www.google.co.kr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0ahUKEwiMq-eN3pzMAhVEj5QKHZfTCrgQFggfMAE&url=https%3A%2F%2Fwww.researchgate.net%2Ffile.PostFileLoader.html%3Fid%3D55d595da5f7f7174df8b456c%26assetKey%3DAS%253A273835536912384%25401442298887741&usg=AFQjCNGmNeUwNPdw3yvOM5P7dVT9BRaR-A&bvm=bv.119745492,d.dGo&cad=rja
GROMACS is tuned towards desktop systems, while NAMD can scale better over clusters/super computers (The main difference so far I know).
However, there are certain algorithmic differences, but I hope with sufficient sampling, those can be overcome.
Best,
Ayaz
There are many factors to consider: Accuracy (force fields, approximations), speed (approximations, parallelization), methods (classical MD, enhanced sampling MD, MD coupled with free energy analysis), convenience (preparation, analysis), learning curve (manuals, tutorials, community), price (free, commercial), customization (source code, programming language).
both of them resolve motion equation. GROMACS is easier to install in a single computer or in a cluster and have a huge set of instruction to obtain a lot of properties.
Hi,
For beginners, use Desmond from Maestro interface. It is free and completely automated. If interested, see my publications with Desmond.
Most of the previous comments are right. First, you should consider several factors:
1) What you want to calculate? (What properties)
2) How many computational resources do you have?
3) Do you have experience in MD simulations?
4) Just classical simulations, QM/MM, etc?
......
There are many softwares for MD simulations. Usually, NAMD or GROMACS are both convenient. If you are able to use supercomputers with many nodes in parallel, use NAMD, otherwise, use GROMACS. Amber probably has the most robust force field, especially if want to include simulations with DNA and proteins. CHARMM and OPLS-AA are essentially at the same level than AMBER.
Parasuraman aiya subramani
I have run MD in Desmond and successfully analyzed it. Now, I want to run advanced analysis like PCA, Free energy landscape, MMPBSA/MMGBSA calculation, etc. How to perform it. Kindly help.
Ranabir Majumder . Sorry, I do not think these advanced analyses are possible. Try converting to respective formats and analyze in Gromacs or Amber.
Best,
Parasuraman
Parasuraman aiya subramani
Thanks for your kind response. But I am unable to generate md.tpr/ md.edr file which is essential for analysis in Gromacs.
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