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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 4 23:13:56 CEST 2012

On 5/10/2012 1:49 AM, lloyd riggs wrote:

Please choose descriptive subjects and start new email messages when 
posting to mailing lists. This makes people better able to respond to 
you by allowing mail reading software to work properly. Cross-posting to 
the VMD and GROMACS lists when your question relates to conversion of 
file formats between GROMACS and NAMD seems a bit strange, too.

> 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.

I don't understand what the problem is from this description.

> 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.

VMD can just read a gromacs trajectory. What's the problem with that? 
Why do you (think you) need a matching .psf?


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