VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Nov 07 2018 - 12:09:47 CST

Hi Behnam,

.gro files don't contain bond information, so VMD guesses based on atomic distances. I'm going to guess this is a coarse grained system, since the atomic distances are much greater in those systems and VMD in that case tends not to work very well. Basically, you need to use your .top file or .tpr file to produce a file that VMD can read in for the bond information. Some options include:

Using top2psf to make a psf file. http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/top2psf.pl

If you are using a coarse grained system, the Martini folks have some tools to make visualization easier:
http://cgmartini.nl/index.php/tutorials-general-introduction/cgviz
http://www.cgmartini.nl/index.php/rb

If you are crazy like me and compile your own VMD, you can use either my .tpr loader (https://github.com/jvermaas/vmd-tprreader) or the .tng support VMD includes to load gromacs files directly.

-Josh Vermaas

On 2018-11-07 02:30:56-07:00 owner-vmd-l_at_ks.uiuc.edu wrote:

Dear all
Unfortunately when I import gromacs output .gro into VMD, it does not recognize residues properly and displays molecules as broken ones. How can I solve this problem?
Thanks in advance.
Looking forward to hearing from you.
Sincerely,
Behnam Ghalami Choobar 

--
Behnam Ghalami Choobar
PhD Candidate in Chemical Engineering
Amirkabir University of Technology, Tehran-Iran