[gmx-users] gmx-users] Atoms Exploded

[Albert Sun]

Dear  Anton
I used VMD to view the .trr file, my problem was :
I first loaded  .gro fiel, it was OK to see the atoms clearly, then when I loaded the .trr  file, all the picture of atoms disappeared immediately.
 
What is the cauese?
 
Thanks
 
Albert
 
 
 


Anton Feenstra <feenstra at chem.vu.nl> wrote:
Albert Sun wrote:
> Dear Users,
> When I simulated a simple 9 atoms system, simulation (mdrun) was completed, but the .trr picture show that atoms disappeared suddenly and can not see anything from the first frame.
> 
> Appreciate if you could advise me how to modify (.mdp or .top or other files) so that I can see the picture from the first frame?

I don't know what you mean with '.trr picture'. What program(s) did you
use to look at the first frame? Possible options would include ngmx,
trjconv, vmd (not a Gromacs program).


-- 
Groetjes,

Anton
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
|_____________|_______________________________________________________|


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