[gmx-users] unable to display MARTINI system with VMD

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 20 03:18:55 CET 2011

The problem is a mismatch in the contents of the .gro/.xtc and .psf produced by 
top2psf.pl.  Since the script only handles one moleculetype, you can only 
display and/or read coordinates of that same moleculetype.  So, to display properly:

1. Strip only the protein's coordinates from the .xtc and fix PBC suitably (the 
one you provided me with is not very useful for visualization - the protein is 
flying all around)

2. Strip the protein's coordinates from your .gro

3. Load the .gro in VMD, then the .psf as data for it, then the protein-only 
.xtc as data for the .gro.

I followed these steps (aside from proper PBC) and your protein loaded just fine.


John wrote:
> Thank you for offering help. I know your script is doing it's job, the 
> problem lies with me. for some reason i cannot figure out where i am 
> going wrong. i am attempting to look at a 163 residue, 2 domain protein 
> (hPin1) and this is on of the domains by itself (only 39 residues).
> i'm attaching a .gro, .itp, .top, and an .xtc for a short 10ns run. i am 
> definitely a beginner when it comes to both GROMACS and MARTINI. I am 
> trying to get a few molecules toward some production simulations with 
> the MARTINI model. for this domain i have something strange happening 
> around 3ns. the rmsd for the protein nearly freezes to a straight line. 
> i am trying to visually see what is going on in the hopes that that 
> might allow me to figure out what the heck to do next.
> i really appreciate your help a lot. i am sort of isolated, lately, from 
> anyone i can discuss anything regarding simulation issues.
> best,
> john


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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