MD was done in desmond, using .gro file and .xtc file to generate .tpr file and .top file

User discussions
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1

dear all
can you help
i run the MD in desmond for 100ns, and am able to generate .gro file by VMD and .xtc file by Gromacs but am not able to generate .tpr file and .top file and .edr. , may aim to do some analysis using Gromacs. attached file in this URL is MD file .dcd .gro .xtc. pdb
also
https://topol.top/
not working
thank you

2

I’m not sure if anyone here knows how convert Desmond input and output to GROMACS formats. To generate a .tpr file you would need to set all the simulation parameters you used in Desmond (provided that there is a 1:1 correspondence), and the force field you used must be available in GROMACS. I’m not sure you would generate the .edr file at all as I don’t know how Desmond stores observables.

Unless someone else knows how to do this, I’d recommend trying other tools for analysis. Does MDAnalysis work with Desmond files?

3

dear MagnusL thank you
Desomd uses only OPLS force field and it is available on GROMACS, unfortunately, MDAnalysis does not work with Desmond files. GROMACS can be plugin to PyMol open source for some reason I don’t know why it not works for me in both Windows and Linux Ubuntu

4

But doesn’t Desmond use OPLS2 or even OPLS3? Those force fields are not (easily?) accessible in GROMACS.