[Chimera-users] Blank screen after MD simulations

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 27 14:39:21 PST 2021

Hi Srigouri,
	The black frames are typically symptomatic of a system that "blew up", i.e. some atoms were not correctly parameterized and consequently wound up directly on top of one another during the simulation, which results in an infinite energy and immediately thereafter coordinates that go to infinity; hence the black frames.
	Chimera and the Molecular Modeling Toolkit (MMTK) that it employs can always correctly parameterize standard amino and nucleic acids (and water), so it would be other molecules in your system that are producing the parameterization problem.  If these other molecules are not important to your reason for running the simulation, you could simply delete them before beginning the entire MD process.
	If they are important, then you would have to use a more expert-level simulation package in order to develop the proper set of parameters and run your simulation -- which will be quite challenging.  Some example simulation packages include Amber, Gromacs, Namd, Charmm, and OpenMM.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Dec 26, 2021, at 8:48 AM, Sri Oruganty via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I am a senior in high school, and I was interested in learning about proteins and mutations. I download Chimera to run MD simulations on a specific protein, but not all the frames are loading. After the frame number gets to a certain point (i.e. 14) every subsequent frame is completely blank. Why is this happening? 
> Best regards,
> Srigouri Oruganty
> Pronouns: She, her, hers
> sri.oruganty at gmail.com <mailto:sri.oruganty at gmail.com>
> (610)-207-6325
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