Re: Strange Bond Behavior Question

From: João Ribeiro (
Date: Fri Jun 22 2018 - 16:08:07 CDT

Hi Kelly,

that really sounds strange, especially because "They seem to be stretching
and bonding to other lipid atoms"
 vague and creation of bonds is impossible.
​ ​
Now, if you generated the bilayer in CHARMM-GUI, I am pretty sure that the
boundary conditions will be wrong. QwikMD doesn't have a way to detect the
axis of membranes generated by other programs, so I will assume that you
have water surrounding your system, even the hydrophobic region of the

What happens if you run the simulation with the psf and pdb files generated
by CHARMM-GUI? Do you observe the same? If you don't, I would suggest for
you to use those psf and pdb files with the configuration files originated
by CHARMM-GUI, or use QwikMD configuration files as templates, changing the
necessary information about your system.



On Fri, Jun 22, 2018 at 3:46 PM McGuire, Kelly <> wrote:

> 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*

João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
+1 (217) 3005851

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