How to install g_mmpbsa in gromacs 2020?

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Problem in energy minimization using Gromacs?

I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.

18 February 2021 4,822 2 View

RDF calculation of water inside the Carbon nanotubes?

I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...

17 February 2021 1,066 3 View

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...

15 February 2021 5,561 3 View

Luis Fernando Cofas-Vargas

Try using GMXPBSA (https://github.com/aspitaleri/gmxpbsa).

Another option is https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.

Good luck!

Ricardo J Ferreira

Hi,

you can dowload the pre-compiled binaries from https://rashmikumari.github.io/g_mmpbsa/ and put it inside GROMACS bin folder. However, they are not compatible with .TPR files generated with GROMACS2020, so you have to use GROMACS 5.1.7 or GROMACS2016.

Nabanita Mandal

Luis Fernando Cofas-Vargas Thanks for sharing the link. I downloaded the tar.gz file of gmx_MMPBSA. But , it is not getting installed properly. Do I need to install anything else before installing it?

Madhusudan Dutta

Nabanita Mandal I think gmx_mmpbsa may be better choice than g_mmpbsa for gromacs 2020. Read this ....

gmx_MMPBSA: A New Tool to Perform End-State Free Energy 2 Calculations with GROMACS

Mario S. Valdés-Tresanco

Moisés Maia Neto We appreciate that you duly report the problem on GitHub, the Google group, or to our emails directly, to provide a solution. We have extensively tested gmx_MMPBSA from desktop to HPC. In fact, it is currently installed at the University of Louisiana and one of the largest service HPCs in China, as well as several HPCs from research groups in India, Brazil, the USA, Pakistan, and Canada, just to name a few.

Moisés Maia Neto

Mario S. Valdés-Tresanco I was able to perform the calculation using all threads by adding --use-hwthread-cpus in the command. I jumped into the comment. I will withdraw. Congratulations on your work. At the moment the challenge would be to use the GPU in the calculation in order to reduce the time even more. I use the GPU in molecular dynamics with gromacs but I still don't know if I can also use it in the calculation of mmpbsa.

Mario S. Valdés-Tresanco is there any command like -nb gpu i need to add so it uses gpu in the calculation with gmx_mmpbsa?

Moisés Maia Neto Currently, gmx_MMPBSA does not support GPU calculations. However, we already plan to implement some PB and GB models on GPU, although this will take some time.

Harvinder Singh

Nabanita Mandal you can try Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...