Can anyone guide me through analysis of Steered Molecular Dynamic in Gromacs?

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Manoj Patel

I dont know much about GROMACS but if you could use already generated gmx files as an input (after converting to appropriate format) into NAMD/VMD analysis then I think you can get some sort of analysis.

If possibel you can attempt same study in NAMD also. Well documented tutorial pdf is available

https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win.pdf

Satyendra Singh

Steered Molecular Dynamics (SMD) is a powerful technique to study the mechanical properties of biological macromolecules. Here is a brief guide to analyzing the output from SMD simulations in Gromacs:

Generate a .tpr file: You will need to create a .tpr file to carry out the analysis. This can be generated using grompp command.

Define the reference group: The reference group is the group that you are pulling. It could be a single atom, a group of atoms, or the whole protein. You can define this in the .mdp file.

Define the pulling group: The pulling group is the group that is used to pull the reference group. You can also define this in the .mdp file.

Extract the distance: You can use the gmx distance command to extract the distance between the reference group and the pulling group. You will need to do this for each time step.

WHAM analysis: You can use the gmx wham command to analyze the extracted distances. WHAM is used to estimate the potential of mean force (PMF) along the pulling coordinate.

Plot the PMF: You can use any plotting software to visualize the PMF. The PMF represents the free energy landscape of the system along the pulling coordinate.

Regarding the incomplete output from gmx wham, make sure that you have provided the correct input files, including the distance data. You may also want to check if the number of data points is sufficient for the WHAM analysis.