[gmx-users] PSF files from .top to .psf

Donovan B.T. B.T.Donovan at soton.ac.uk
Mon Mar 28 19:06:05 CEST 2011

Hi All

I'm trying to measure some dipole moments in VMD using "measure dipole", but am having trouble with the .psf file format. I'm not sure that the conversion tool [top2psf] is coping with the .top file and its three .itn include files. I have tried numerous work around's for include files [by pulling them out into the .top file], but I cannot seem to find a way to get the .psf, .gro and .xtc formats all loaded correctly into VMD. Native conversion of the .top [includes extracted] into .psf doesn't work and nor does converting each .itp file individually and concatenating.

The biggest hurdle is finding a suitable script for how I should format the .psf file, for example I have lipids and a solvent. Do I have to describe each and everyone of the lipids in the system and the same question to the solvent. Apologies for the ask, but I could find nothing other than quite simple molecules with no solvent as examples for .psf.

Best wishes and thanks


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