Hello all, I want to plot lateral stress map from MD simulation of lipid bilayer i.e I want to plot local stress of bilayer as a function of x and y. Is there any Gromacs module or external tool that I can use? Thank you.
Gromacs-ls (https://www.mdstress.org/index.php/gromacs-ls/) should do what you want. Its essentially a rerun option that gives you the stress tensor (gld, cfd ...)
Hello Otto Schullian ,
Thanks for your suggestion.
I have installed the program and is running. But it is taking quite a long time to analyze each frame. Can you suggest any way to reduce the computational time? That would be really great.
- Anirban
Hello Anirban Paul ,
Unfortunately I am not sure that is really possible. In order to calculate the stress profile the program needs to recalculate all the interactions and that is a tedious and long job. You can consider splitting the trajectory into pieces and have the calculations being done in parallel.
When starting the -rerun with gromacs-ls you can turn off certain contributions (like kinetic, non-bonded, angles etc.) and you can check which contribution takes so long. It however does not really tell you how to fix it.
Another option you can consider is cutting the long-range interaction (usually coulomb) as that is very tedious. That might make it faster, however, one should be extremely careful if the stress calculation is not done with exactly the same forces as the simulation itself. Artefacts, such as non-divergence-free stresses for equilibrated systems can appear, which is necessarily wrong.
Finally there is another potential code you can use, published here (Article Pressure Profile Calculation with Mesh Ewald Methods
), where they implemented a different contour for the calculation and this works with PME. I have not worked with this yet, so I can't tell you whether it is faster. But again, one should be careful that both stress calculation and the simulation use the same forces, otherwise strange things can happen, and with pressure they are not easily spotted (I usually notice them at a later stage when I calculate mechanical properties such as surface tension).I am sorry this might not really help, but if you have any more questions just write
Best
Otto
Thank you so much Otto Schullian for your valuable comments and suggestions.
In the manual they have said the program is not using any GROMACS optimization and thus much slower. I will definitely try to make it parallel and also look into the paper.
Thanks a lot!
- Anirban
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