Strange Bond Behavior Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Jun 22 2018 - 15:42:20 CDT

This is a question for both VMD and NAMD support, so I am sending it to both. I used QwikMD to set up a simulation, and

something I have never seen before has occurred. I placed a membrane protein in a 100x100 DMPC bilayer using

CHARMM-GUI, and then I used that PDB to set up a simulation in QwikMD. Upon observation of the minimization, annealing, and

equilibration DCD files, I noticed the lipid bonds doing something very odd. They seem to be stretching and bonding to other

lipid atoms. I tried attaching pictures, but I don't see it posted to the mailing list. I didn't change anything in the minimize, anneal,

and equilibrate scripts that QwikMD produces, and I've never seen this before with those simulations with these generated scripts...

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

This archive was generated by hypermail 2.1.6 : Thu Dec 05 2019 - 23:19:57 CST