[MMTK] Questions on nMoldyn trajectory conversions and Sqw units

Hartling, Kathryn kathryn.hartling at cnl.ca
Tue Jul 19 14:49:50 UTC 2016


Dear nMoldyn users,


I have two questions:


1.       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). 

Does anyone have experience using nMOLDYN with GROMACS? If so, could you please let me know how you converted the relevant files to MMTK format?

2.       The documentation on the dynamic structure factors (coherent and incoherent, DCSF and DISF) in the nMoldyn User's Guide suggests that the output should have units. However, when I use ncdump on the generated .nc  file, the Sqw ouput is listed as unitless. Could someone confirm exactly what form (and units) of the dynamic structure factors are being output by the DCSF and DISF functions in nMoldyn?


Thanks very much, 





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