VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Oct 23 2020 - 03:33:17 CDT

Thanks for the response! Each DCD is about 10 GB. So, 500 GB for the whole trajectory.

Haven't ever tried qwrap. I thought it was mostly for orthorhombic water box shapes. Maybe it's worth a try.

I couldn't attach the pictures to the first email. Is there a way I can send them to you for better context of the description in my email? It might clarify the problem a bit more. 2-3 of the segments are hanging outside of the water box on one side and the 4th segment is hanging outside the water box on the other side. Can't seem to get all segments back together in the center of the box no matter what set of commands I use....

Dr. Kelly L. McGuire

PhD Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: René Hafner TUK <hamburge_at_physik.uni-kl.de>
Sent: Friday, October 23, 2020 2:25 AM
To: McGuire, Kelly <mcg05004_at_byui.edu>; VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: PBC Wrapping

Dear Kelly,

First recommendation:
    Use Jérôme Hénin qwrap tool for wrapping/unwrapping of trajectories.

    https://github.com/jhenin/qwrap

It is a lot faster than the pbctools wrap command. (:

2. What file sizes are we talking about here? Dozens of GB or TB?

>From my point of view:

    If you have a PC or cluster node with enough RAM it might be better to load the whole 2µs DCD at once.

I'd say if the simulation ran properly regarding the Box size (NVT I guess) there shouldn't be too much of a problem regarding wrapping the trajectory. It might just be that the dynamics are unreasonable if the protein segment interact with other parts of themselves by PBC and therefore may invalidate the results.

Kind regards

René

On 10/22/2020 11:06 PM, McGuire, Kelly wrote:
I know many people have asked a similar question and the topic is quite exhausted. However, I have tried multiple combinations of PBC wrap that I have found int he mailing list or in the manual and they aren't working this case.

Problem Background:

I just started a postdoc and have been asked to help one of the grad students to get the protein joined back together and re-centered in the water box. He has run a 2-microsecond simulation of a multimeric protein (4 segments) in a water box. Two problems I noticed immediately is that his water box is too small for the protein (in my opinion) and second, he did not have wrap turned on in his config file. He has chopped this 2-microsecond simulation into 40-nanosecond long DCD files, so he has 50 DCD files that need to be wrapped. In some of the DCD files I can get the protein joined back together and re-centered, but there are many that I cannot. I have pictures of one such very difficult case (email won't go through with attachments, how to send pics?). Blue is segname PROA, Red is segname PROB, Orange is segname PROC, and Green is segname PROD. These pictures represent ~1.8-microseconds into the simulation. Pic-1 and Pic-2 are the first frame (front and top-down views respectively). Pic-3 is the top-down view of the last frame. All of the protein segments are constantly close to the boundary conditions. I can only get 2-3 of the segments to join back up before centering the water box. There is always one of the segments that won't join back with the rest of the protein.

Questions:

1) Is it possible to do a wrap on the whole 2-microseconds DCD files at once? Meaning load all of the DCD files and wrap the protein? Or is it better to do each DCD file individually?

2) Is this an impossible case to wrap because the water box is too small?

3) Any specific suggestions on how to get this protein put back together and re-centered?

4) In the first few DCD files, I used:

pbc wrap -center com -centersel "protein and segname PROB" -compound residue -all

pbc wrap -center com -centersel "protein and segname PROD" -compound residue -all

pbc wrap -center com -centersel "protein" -compound residue -all

This worked just fine. Why would this not work for all 50 DCD files for the whole 2 microseconds? Are different wrapping commands needed for each DCD of the same long simulation?

Dr. Kelly L. McGuire

PhD Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602 

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Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany