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

[Donovan B.T.]

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


Brett

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From: Donovan B.T. <B.T.Donovan at soton.ac.uk>
Subject: PSF files from .top to .psf for use in VMD
Date: Mon, 28 Mar 2011 15:20:47 +0100
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