Re: vmd-l: Re: Strange Bond Behavior Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Jun 22 2018 - 21:27:04 CDT

Thanks for the information! Mike, would not using the extended PDB format effect my simulation results in any way, or is that just a VMD visualization issue and not a simulation issue?


Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602


________________________________
From: Mike McCallum <mmccallum_at_PACIFIC.EDU>
Sent: Friday, June 22, 2018 7:37:57 PM
To: McGuire, Kelly
Cc: João Ribeiro; namd-l_at_ks.uiuc.edu; Vmd l
Subject: Re: vmd-l: Re: namd-l: Strange Bond Behavior Question

I think this means that the algorithm is making some bad choices in deciding what a bond is. The bonds are only well-defined between specific atoms from the PSF. So you are not getting that information in the PDB+DCD case. While there is a extended PDB format which includes bond definitions, I don’t believe they are written using charmnGUI, and in any case VMD does not read them.

Mike McCallum
mmccallum_at_pacific.edu<mailto:mmccallum_at_pacific.edu>
cmccallum_at_mac.com<mailto:cmccallum_at_mac.com>
cmikemccallum_at_gmail.com<mailto:cmikemccallum_at_gmail.com>

On Jun 22, 2018, at 3:43 PM, McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:


One more thing I should mention. I loaded the DCD onto the PDB file and that's when I see the odd effects. However, if I load the PSF and load the DCD onto that, I don't see those strange bond effects. What does that mean?


Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602


________________________________
From: João Ribeiro <jribeiro_at_ks.uiuc.edu<mailto:jribeiro_at_ks.uiuc.edu>>
Sent: Friday, June 22, 2018 3:08:07 PM
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>; McGuire, Kelly
Cc: Vmd l
Subject: Re: namd-l: Strange Bond Behavior Question

Hi Kelly,

that really sounds strange, especially because "They seem to be stretching and bonding to other lipid atoms"
is
 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 membrane.

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.

Best

Joao


On Fri, Jun 22, 2018 at 3:46 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> 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
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu<mailto:jribeiro_at_ks.uiuc.edu>
+1 (217) 3005851

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