[gmx-users] visualizing the system

[Shima Arasteh]

Hi,
I am simulating a system composed if POPC , peptide, waters and ions.
I used the InflateGRO methodology to construct the system.
There are 2 phenylalanine residues in my peptide. Each phenyl has 2rings connected from one side. After inflategro one of the phenyl rings is normal, but the other is not because  What I see them in vmd, there are 2rings remain close to eachother but the expected bonds between them are not visible.
The top file shows the correct bonds and angles and ... .
I ran EM, NVT, NPT, and thought this problem would be solved but it is still as well as before.
The EM was also ok and did not show high enegy or crash.
Does this problem relate to the vmd and its algorithms? Or there is a problem with my system.
How would the rings look usual? How could I solve it?

Thanks in advance.
Sincerely,
Shima