[gmx-users] Re: vmd-l: Re: compiling VMD with gcc 4.7

lloyd riggs lloyd.riggs at gmx.ch
Thu Oct 4 17:49:33 CEST 2012

Dear All,

I spent two days converting a .top file from gromos53a6 to one readable by VMD/NAMD.

Now I am about to begin the ffbonded/nonbonded to a readable format for the same and would like to know beforehand if anyone has already done this so I can just use the library?  Most are straightforward conversions of format.  The main prblem is the NAMD (I believe) does not already have the parameters for cg or merged CH croups.  The gromos force fields for gromacs only do this with chain non-polar, leaving the charged H groups alone.  I did find however, no equivalent with trying to first generate a .psf file, and then looking at the vdw /angle, dihedrals and non bonded files for NAMD.

Example a methyl is CH3 with a mass of 15.00 CH2 Mass 14 ,etc  with only 3 atom type changes, you would think it wouldnt be so painfull, but it turns into a hellish nightmare.

Any links or pointers would be appreciated, however I already assume I have to do this myself to use the VMD tools with Gromacs traj.  Its still shorter than 3 months of simulations with a new index file.


Stephan Watkins

More information about the gromacs.org_gmx-users mailing list