[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.
> 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.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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