Hello.

Check GROMACS (www.gromacs.org). In my profile, you will find an article about membrane protein simulation (DOI: 10.1021/ct300083m), more specifically ABC transporters (P-glycoprotein) on a POPC membrane. This paper have all the steps/methods you will need.

Any help on membrane building or any other issue, please ask.

Best regards.

For molecular dynamics for proteins specifically, I would suggest to start with Gromacs, preferably in Linux OS. Gromacs is command-line and well suited to learn and Academic research. AMBER is the best for proteins and free license for academia.

I would suggest you to surf the net, for other tools. Check the link to have basic idea http://en.wikipedia.org/wiki/Category:Molecular_dynamics_software

All the best

Amber is not free but cost only 400$ for academic. Definitely I suggest Amber 12 and especially GPU code, just see the benchmarks:

http://ambermd.org/gpus/benchmarks.htm#Benchmarks

Thanks to Ross's group we are able to perform something that was possible only for those that have access to supercomputers. Moreover Amber is one of the most reputed code and has many advantages!

I suggest you CPMD, CP2K, AMBER, Gromacs it depend on what you want to simulate axactly (small molecules , peptides, protein....)

I am working on membrane proteins

Poornima, NAMD is free, I had worked on it, I am searching for more MD softwares

Amber is best for starters and have very good online tutorials and have very helping mailing list as well. Even for membrane proteins now they are benchmarking forcefield. Charmm is considered best for membrane till now but you cant use with AMBER but gromacs has the option to choose the forcefield. Desmond is also very good (free) software and fast as well

It depends on what kind of system do you intend to simulated. One of the best all-atom MD code would be LAMMPS (it can be used for various simulation levels) but someone may consider also Dl-Poly, Desmond and Gromacs. All of them are very efficiently parallelepiped. For coarse-grained simulation you may try VOTCA, IBiSCO or OCCAM (sure, also LAMMPS and Gromacs).

Try NAMD, Its freely available for academia and very well documented as well.

The details can be found at http://www.ks.uiuc.edu/Research/namd/

Good luck

VMD can be used as GUI for NAMD. The details are at http://www.ks.uiuc.edu/Research/vmd/

again free software

Desmond is another freely available software for academia with Maestro as a GUI provided by Schrödinger.

Details are at;

http://www.schrodinger.com/productpage/14/3/

http://www.deshawresearch.com/resources_desmond.html

http://www.schrodinger.com/downloadcenter/10/

Hope this will help you

Other commercial software for MD simulations are,

Amber,

MOE,

Discovery Studio etc

Some of them are linked to NAMD or Desmond

Hello.

Check GROMACS (www.gromacs.org). In my profile, you will find an article about membrane protein simulation (DOI: 10.1021/ct300083m), more specifically ABC transporters (P-glycoprotein) on a POPC membrane. This paper have all the steps/methods you will need.

Any help on membrane building or any other issue, please ask.

Best regards.

You may also want to check out OpenMM (https://simtk.org/home/openmm), which is open-source and free to download. It's optimized for high performance, especially on recent GPUs, and emphasizes flexibility, providing you the ability to include custom forces and integrators.

Thankyou Joy Ku this is good site

Great suggestions by all the above posts, I recommend you to go for GROMACS, as you are already working on it.

If you need a powerful, flexible, free, comprehensive manual and extremely high level MD simulation code, get the LAMMPS.

http://lammps.sandia.gov

Most of the MD codes have similar features, but the real differences consist in their speed, parallel scalability and the class of the force fields. LAMMPS is the one that reach the maximum points regarding the three aspects. It can be used as standalone code or as library, and can include several external modules. Maybe, GROMACS is very suitable for biological systems as it has various force fields developed for the biological systems, and has several additional tools for system preparing and analysis.

You can try NAMD. It is free, various tutorials are available.

http://www.ks.uiuc.edu/Research/namd/

Yes, of course, NAMD is quite useful tool and relevant to the query.

We have to not forget DL-POLY (http://www.stfc.ac.uk/CSE/randd/ccg/software/DL_POLY/25526.aspx), which is a great MD code. Another very good MD package is GULP (http://projects.ivec.org/gulp/). It is not very efficient for very large systems but it contains great tools, like energy minimizer, transition state identification, potential parameter fitting, mechanical and thermodynamic properties for 0-3D periodic systems. It can be coupled with quantum codes in Chemshell for QM/MM calculations.

Both codes are free, but require the registration.

Thankyou for the information

Another - Abalone

http://www.biomolecular-modeling.com/Abalone/index.html

The main is that, what kind of simulation you want to do.

Otherwise there are several free MD codes (e.g., Lammps, Namd, Gromacs, Amber and ..)

In our work we have used NAMD/VMD (and tools) with excellent results.

I think GROMACS is among the best free software programs for MD simulation and is actively developed. Good luck.

Rank by performance (TOP SOFTWARES)

W=Windows

L=Linux

F=Free

C=Commercial

SCHRODINGER C-W-L

Discovery studio - C-W-L

MOE C-W-L

GROMACS F-L

AMBER C-L

Abalone F-W-L

Ascalaph Designer F-W-L

YASARA C-W-L

VMD-NAMD F-W-L

YOU CAN FIND A COMPLETE LIST HERE:

http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling

ACEMD works very well also and it is about 10x faster than NAMD.  I think it is the fastest. There is a free version of the software.  Google will direct you to it.

for polymer which MD simulation software gives good results.

Hi all

which MD simulation software is user friendly in windows OS

Hello

Gromacs package or Amber package

Hi Mahnam

Will you please let me know the steps to run Gromacs

 Dear Pritam

Thanking you very much for your kind

Materials Studio is an excellent user-friendly software for modeling. LAMMPS is suitable for running simulations. VMD help us in visualization. 

It depends to the system which you want to study. In the case of proteins, you may try NAMD, and for material studies , Lammps is good.

Is Materials Studio a free software ?

Materials Studio is a commercial package of programs and it is quite expensive, but you can buy only some modules.

Hello ,

how can we do molecular dynamics simulation of a docked protein + ligand file?

Dear Pritam

Thank you very much for the detailled explanation of using gromacs

My question is Can you give a step by step example of molecular dyamics of inorganic material using gromacs

How can I install GROMACS on windows? I have a very poor idea about compiler. That's why I am unable to understand the instructions in GROMACS website. Please please help me. Please supervise me to prepare my windows 7 PC for GROMACS {if any other software required for it}.

I want to simulate semiconductor interface for heat flow.

which tool would be good?

please suggest me a MD tool.

in very cases GROMACS is most rapid and user friendly in comparison to other softwares. Specially in biological system , GROMACS is unique

for electrical properties my suggestion is quantum espresso

LAMMPS is a robust open-source molecular dynamics software. It has many features and it's easy to extend with new features and functionalities.

how can we do molecular dynamics simulation of a plastic recycling and using which tool?

GROMACS is somehow specific to bio-systems, the LAMMPS is generally applicable to materials science

Thank you for the reply Viorel Chihaia .

I have tried lammps, gromacs, namd and charmm when I just started to learn and do classical molecular dynamics simulations, out of these 4, lammps is the best, easy to learn, well documented, wide community support, plenties of force field models available, acceptable speed on clusters, easy to add/modify source codes for your own purposes, and it is free

Hi, Try using webgro from the link posted below. It is a tool which uses gromacs for its protein simulations. Great tool which is free to use for protein simulations.