[gmx-users] RE: problem with using VMD to view the trajectory

[Vitaly Chaban]

> I am a new user of gromacs. Recently, I have installed the gromacs-3.3.3 software package on my computer. After installation was complete, I run the example of water in
> the online reference manual. The trajectory file is OK for the first time. But when I run it for the second time, and used vmd to look at the trajectory, I found that the trajetory is >disordered, the frames in the VMD main are equal to 2, and the output file .gro seems ok. What's worry with my gromacs? I don't know what to do now and how can I overcome >this. Could you help me?

If the trajectory was OK for the first time everything is very well
with your example. I would suggest just to rerun your task and pay
particular attention to the type of file you submit to VMD (trr, xtc).

What means "trajectory is disordered"? Is everything OK with your
settings of PBC?

-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban