VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Oct 04 2012 - 13:25:24 CDT

Dear Lloyd,

Could you please tell us what is the connection between your message, the vmd list and the thread that you are replying to?

Please be more careful when sending emails. The subject of an email is an important field used to sort and classify mails. Also please avoid cross-postings.

Thanks for understanding
Vlad 

---
Dr. Vlad Cojocaru
Max Planck Institute Muenster
Roentgenstrasse 20,
48149 Muenster, Germany
Tel: +49-251-70365324
Sent from my mobile phone; Sorry for being short and for any errors
lloyd riggs <lloyd.riggs_at_gmx.ch> wrote:
>
>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.
>
>Sincerely,
>
>Stephan Watkins