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

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 20 02:33:17 CET 2011

John wrote:
> Hello,
> I have run a few protein systems through simulations of varying lengths 
> and would like to find a way to visualize the trajectories. I have tried 
> to use the top2psf.pl <http://top2psf.pl> script to produce a usable 
> .psf file. I can get it to produce the .psf file, but am unable get VMD 
> to display anything for the trajectory other than a bunch of dots.

If you send me your input files (off-list) I will try to debug it.  For most 
simple cases, the script should produce usable output.

> anyone had any luck displaying MARTINI trajectories with VMD and might 
> know where i am going wrong? any suggestions are very appreciated.

There's a Tcl script from the same site where you (presumably) found my script, 
but I've never used it so I can't help you with that.


> -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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