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 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 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
