When you try to chose which software to use for running MD simulations, there are a few criteria that you may prioritize, such as:
1) possibility of modeling different biomolecular systems (e.g., protein, membranes, DNA, RNA and their complexes);
2) possibility on modeling the solvent environment explicitly and/or implicitly (water, ions, etc,);
3) flexibility on using different force fields for parametrization of the systems and efficient treatment of long-range electrostatic interactions;
4) computation efficiency (in terms of speed) for running long time dynamics (e.g., is the code parallelized, can you use GPU, etc,);
5) possibility on running the simulations in different statistical ensembles (e.g., NVT, NPT) and possibility of using different periodic boundary conditions based on the geometry of the simulation box;
6) implementation of stable numerical integrator methods for solving equations of motion;
7) being easy on building up equilibration protocols (e.g., through documentation and tutorials);
8) providing tools and/or modules for analyzing the trajectories;
9) being able to create outputs in a format which can be easy read from other data visualization and/or analyzing software;
10) being able to read and manipulate the inputs structures (e.g., PDB format files);
11) in some cases, being able to compute complex thermodynamic properties, such as free energies, using advanced molecular dynamics methods;
12) implementation of efficient conformation sampling algorithms;
13) and maybe others (depending on the problem).
Some molecular dynamics engines that satisfy the above mentioned criteria include CHARMM, GROMACS, NAMD, AMBER, DESMOND, TINKER, DL_POLY, and maybe others.
I hope that this helps this discussion!
In my opinion VMD was primarily developed for visualization purpose. GROMACS is specialized for MD experiments. One can also analyze results obtained from GROMACS in VMD.
There is some loser who is reading this discussion, instead of extending the discussion with open mind to expand our knowledge horizons, he is just pressing 'downvote' button for everyone of us. Literate people express their opinions substantiated by arguments. They do not malign other people. It is the forum to discuss and learn from each other. This platform gives us rare opportunity to connect diverse kind of people with variety of expertise in different fields and it is really helpful.
When you try to chose which software to use for running MD simulations, there are a few criteria that you may prioritize, such as:
1) possibility of modeling different biomolecular systems (e.g., protein, membranes, DNA, RNA and their complexes);
2) possibility on modeling the solvent environment explicitly and/or implicitly (water, ions, etc,);
3) flexibility on using different force fields for parametrization of the systems and efficient treatment of long-range electrostatic interactions;
4) computation efficiency (in terms of speed) for running long time dynamics (e.g., is the code parallelized, can you use GPU, etc,);
5) possibility on running the simulations in different statistical ensembles (e.g., NVT, NPT) and possibility of using different periodic boundary conditions based on the geometry of the simulation box;
6) implementation of stable numerical integrator methods for solving equations of motion;
7) being easy on building up equilibration protocols (e.g., through documentation and tutorials);
8) providing tools and/or modules for analyzing the trajectories;
9) being able to create outputs in a format which can be easy read from other data visualization and/or analyzing software;
10) being able to read and manipulate the inputs structures (e.g., PDB format files);
11) in some cases, being able to compute complex thermodynamic properties, such as free energies, using advanced molecular dynamics methods;
12) implementation of efficient conformation sampling algorithms;
13) and maybe others (depending on the problem).
Some molecular dynamics engines that satisfy the above mentioned criteria include CHARMM, GROMACS, NAMD, AMBER, DESMOND, TINKER, DL_POLY, and maybe others.
I hope that this helps this discussion!
You can use GROMACS, AMBER or DESMOND (academic version).
and the criteria for selecting the software are very well explained by Hiqmet Kamberaj
Dear Som,
You have been provided with lots of information now it is the time to act. All the best!
Hi
Im a bit late to get post but might be helpful.
As somebody that had no previous experience in MD, I had no idea where to start.
I have sinced used Gromacs, AMBER and Desmond. Some of my thoughts; As mentioned before it depends on what you want to simulate and which force field would fit best. But more importantly for me, what type of analysis you would like to do. The tutorials on AMBER I found the best as a novice, but there are more information available on Gromacs. The analysis tools available on these two are very powerful but you would need to know what you would like to do with the trajectories. Using these programs really help in understanding what is happening at each step, from the setup through the minimisation to the production.
Desmond and it's GUI does save a lot of time if you do not know how to use a terminal and the analysis tools such as the simulation interaction diagram is perfect if that is what you want from the data.
There are many other factors to consider as well, but I would try as many of the different software as possible (all that ticks the boxes explained by Hiqmet Kamberaj) to find one that fits your needs.
All the best.
I use ESPResSo for Molecular and Langevin Dynamics. It includes a lot of features discussed here (see http://espressomd.org/wordpress/). What is important for me is that it is open-source in a most conventional modern meaning and always being developed further and well-supported by the community.
In different systems , several softwares can be the best
but in very cases GROMACS is most rapid and user friendly in comparison to other softwares. Specially in biological system , GROMACS is unique
I will recommend two software, AMBER and GROMACS.
GROMACS is fun and is comparatively much easier to learn and post-analyze the simulation. However, you might have to deal with bunch of errors.
On the other hand, AMBER won't bother you too much about the errors but is a bit challenging to practice....Still I prefer GROMACS. Goodluck
hi
i want to to simulate and model crossing magnetic nano-particles through blood brain barrier , which software do you suggest for molecular dynamics?
Hello
https://www.rcsb.org/pdb/static.do?p=software/software_links/modeling_and_simulation.html
Good Luck.
someone can help me to find a free software for Molecular Dynamics and how can I learn about this topic from the very basics. Books, tutorials, etc?
Julio César Velázquez, in regards to a learning of the domain, I would recommend these references [1,2,3]. Please keep in mind what exactly you are interested in: the atomistic level/organic chemistry or meso/nanoscale science or both. The provided references will give a hint. In regards to the software, please see recommendations above in this thread. For the atomistically resolved systems, the well-known software frameworks are GROMACS, NAMD, AMBER, etc. For the spatially and/or temporally coarse-grained systems, I personally use ESPResSo.
[1] Allen, Michael P., and Dominic J. Tildesley. Computer simulation of liquids. Oxford university press, 2017.
[2] Schlick, Tamar. Molecular modeling and simulation: an interdisciplinary guide. Vol. 21. Springer Science & Business Media, 2010.
[3] Satoh, Akira. Introduction to practice of molecular simulation: molecular dynamics, Monte Carlo, Brownian dynamics, Lattice Boltzmann and dissipative particle dynamics. Elsevier, 2010.
Desmond by far for simple tasks. The disadvantage is the lack of protocol programming which is important for ion channels and protein transport in general.
I terms of integration with the rest, I would strongly recommend Schrodinger software with Desmond as a free-for-academia module. You have to install it under Linux and have a decent GPU (NVIDIA P5000 or better) for calculations. Consumer cards work as well but they have problems with intensive calculations by simply warping from the heat.
There is no definite answer to this question. Whatever software people have expertise on, will claim that to be the best. Then there is restriction upon costs, user friendly, handling, etc. so accordingly choose the best for yourself.
1. GROMACS
2. NAMD
3. AMBER
4. Hypercube Hyperchem
5. Spartan
6. Chemoffice
The best as per order and many sottwares available
From popularity point of view, which one is the most popular amongst scientists?
If you are hiring people, which one would be easier to recruit people?
I would recommend GROMACS as it runs effectively on almost any kind of system
I would like to suggest GROMACS for Protein-protein simulation and Desmond module of Schrodinger for Protein-ligand complex simulation.
Desmond/GROMACS... use any of them... Both simulation softwares are very much efficient...
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