[gmx-users] Tryptophan rings are not connected in visualization
shima_arasteh2001 at yahoo.com
Sat May 18 04:08:34 CEST 2013
I am simulating a system composed if POPC , peptide, waters and ions.
I used the InflateGRO methodology to construct the system.
are 2 Tryptophan residues in my peptide. Each Tryptophan has 2rings
connected from one side. After inflategro one of the Tryptophan 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
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.
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