[gmx-users] nMoldyn with GROMACS

[Hartling, Kathryn]

UNRESTRICTED / ILLIMITÉE

Dear GROMACS users, 

 

Does anyone have experience using nMoldyn with GROMACS output? If so, could you please let me know how you converted the GROMACS trajectory to MMTK format?

 

I would like to use nMoldyn to analyse trajectories output by GROMACS. I have converted the GROMACS trajectory output to .dcd format using Wordom, and have tried using the NAMD and CHARMM conversion options in nMoldyn to convert to the appropriate MMTK format. The conversions claim to be successful, but when I load the generated .nc file it seems that the periodic boundary conditions of my system have been lost (nMoldyn recognises an infinite universe). Further analysis operations with nMoldyn don't work properly either. I am not sure whether the problem is occurring in the Wordom conversion or in the nMoldyn conversion step (although I am guessing that the Wordom-generated .dcd file is not in the right format for either nMoldyn conversion option).

 

Thanks very much, 

 

Katy