[gmx-users] image control

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 16 00:10:35 CET 2008

Myunggi Yi wrote:
> Thank you.
> I know general setup to run a simulation, and I'm running one.
> As you see the title, I have problem with image.

Well that was a dozen emails ago and we've talked about many topics 
since. You'll get nowhere fast by assuming that the people you're asking 
for help have the whole email exchange memorized... they have their own 
problems. To get effective help, describe things fully, and if you need 
to refer back to something, go and get a URL to the mailing list 
archives on the GROMACS webpage. This may seem onerous, but you're the 
one trying to get free help, so you maximise your chances by making life 
easier on the people who might give it to you.

> I'm getting broken lipid in the trajectory.

You're not. mdrun doesn't write broken molecules if they were whole in 
the topology. Your visual representation might have them crossing PBC 
boundaries in a way that might make them look broken, however. There are 
many ways to adjust your visual representation, however.

> Would you let me know how to avoid this?

As someone else has already suggested, judicious use of trjconv and the 
.gro file you use with VMD are needed here. Read the man page for 
trjconv and experiment to find what works for whatever your trying to do.

> Do I need special setup?



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