VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Mon May 01 2023 - 13:39:12 CDT

Hi Josh,

Thanks for clarifying, I can see that unwrapping the protein removes any flutters I could see previously. So would that also include things like calculating the hydrogen bonds between the two protein chains? Or would wrapping be necessary for that calculation?

Best,
Christos
________________________________
From: Josh Vermaas <vermaasj_at_msu.edu>
Sent: Monday, May 1, 2023 10:02 AM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Random Sudden Increase in RMSD Near End of Simulation

Hi Christos,

Yes, wrapping chains won't be required if all you care about is the RMSD or RMSF or other quantities that are *just* related to the protein. Wrapping only enters into this when you care about the protein interacting with its surroundings, since then you'd want to make sure that the nearest neighbor atoms are accurate. But if all you want to know is if the protein is stable or not, that is independent of the environment. Basically, if you look at the trajectory in VMD, and it looks like there aren't flutters created by the PBC, you'll be fine. You will likely still need to align your protein though, so that you actually are calculating the minimum RMSD without a rotation or translation component.

-Josh

On 5/1/23 12:43 PM, Efthymiou, Christos wrote:
Hi Josh,

I would like to clarify something. I tried wrapping the whole protein complex, one chain individually, and sequentially wrapping each chain individually, but still had the same issue. However, if I just used the command pbc unwrap -sel "protein", the problem was solved. My understanding is that the command removes the periodic boundary conditions, allowing the protein to stay together rather than being split across the simulation box. Without wrapping the chains after unwrapping, the protein can still drift outside of the box and will not be in the center of the solution. However, for calculations such as RMSD, RMSF, etc. or any calculations only pertaining to the protein component of the system, they should be correct without wrapping the protein chains, right? Please let me know if this is correct or if it is necessary to wrap the chains for all calculations.

Best,
Christos
________________________________
From: Vermaas, Josh <vermaasj_at_msu.edu><mailto:vermaasj_at_msu.edu>
Sent: Friday, April 28, 2023 2:20 AM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk><mailto:christos.dereschuk.20_at_ucl.ac.uk>; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu><mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Random Sudden Increase in RMSD Near End of Simulation


⚠ Caution: External sender

Hi Christos,

If you have a protein complex that is split apart by PBC, you need to put it back together again for RMSD analysis. pbc unwrap is supposed to do this, but may run into issues if there are any frames that do not have periodic box information loaded into them. Trajectory files like dcds or xtcs have these by default, but not all inputs do. Another thing to try is to PBC wrap around *one* of the protein domains. That declares that one domain is the "center", and the algorithm will try and put everything within 1 box of that central protein. If you select over the whole "protein" selection, the center of the selection will be the center of mass of the separated proteins, which is probably in solution somewhere, and isn't what you want.

-Josh

On 4/28/23 02:58, Efthymiou, Christos wrote:
Hello,

I am trying to calculate the RMSD for each frame in my simulation, but I noticed that there are two sections near the end (around 100-200 frames each) where the RMSD suddenly jumps from around 2 to 6 angstroms. I have visualized a portion of the trajectory and it appears that the protein-protein complex is partially crossing the periodic boundary condition and causing this issue. In my script, I have used the command pbc wrap -centersel "protein" -compound residue -all prior to calculating the RMSD. I have also tried using pbc unwrap -sel "protein" -all first, but the issue persists. I also tried having the pbc wrap command happen again 25%, 50%, and 75% of the way through the calculation by placing it within the RMSD calculation loop with an interval, but this still did not solve the issue.

How can I ensure that my RMSD calculation is corrected, and the protein-protein complex does not cross the periodic boundary condition if pbc wrap is not working?

Best,
Christos


--
Josh Vermaas
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io


--
Josh Vermaas

vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io