[gmx-users] a residue move in extremely large scale in MD

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 14 10:24:11 CEST 2012 

On 14/08/2012 5:54 PM, Acoot Brett wrote:
> Dear All,
>
> Thanks for the reply. Then is any single trjconv command available before viewing the trajectory file, or before extracting the xtc file, with that command all the fraud caused by the PBC effect will be got rid of?

I linked a page with a workflow for handling these kinds of issues. If 
there was a magic command that would work for everybody's case then it'd 
probably be there, so probably there isn't one. Maybe a single command 
(or no command) will work in your case, but you're going to have to 
think about it and experiment, because only you know enough to make the 
decisions discussed there. Nobody else is going to be motivated to guess 
how to solve a problem whose existence you haven't even established 
(which you might do by looking at the whole trajectory).

> In addition, the "box" in the e-mail of Dr Dallas Warren should be the solvation box, right? If I am right, usually the dimension of the box is somewhat larger (or much larger) than the protein dimension itself. Thus theoretically it should be rather difficult for the atom of the protein move out of the boundary of the box.

Nope. That page mentions that molecules diffuse. Please read it.

Mark

> If my saying is not correct, please let me know.
>
>   I am looking forward to getting your reply.
>
> Cheers,
>
> Acoot
>
>
> ________________________________
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tuesday, 14 August 2012 2:11 PM
> Subject: Re: [gmx-users] a residue move in extremely large scale in MD
>
> On 14/08/2012 7:53 AM, Dallas Warren wrote:
>> >From your comments, it appears that you have not watched the trajectory for you system.  This is really something that everyone should do with the systems they are simulating, as you can gain a lot of information from looking visually at it.  Looking at 0.5ns snap shots is not watching the trajectory.  What this entails is loading up the .xtc or .trr file for the simulation with something like vmd.  Mine normally have a frame about every 10ps or so, larger step size if it is a longer simulation.  Then sit there are watch it, see how things move around, do things jump, does the angles and shapes look sane etc.
> Yep, this is essential. If I had a dollar for every time I'd seen
> someone waste months of computer time by not watching their trajectory,
> I'd be heading out for lunch.
>
>> The PBC does not effect the simulation as such, what it does do is confuse the analysis scripts if they can't handle PBC correctly.  By watching the trajectory, and even in the snap shots, if the residue is close to the boundary then you will see it "jump" in the visualisation from one side of the box to that other.  It will have only moved a short distance, but due to the PBC that is used with simulations to avoid edge effects it, and the manner in which the simulation software places the coordinates, it can look like it moves significantly.
> Also see
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> Mark
>
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Discovery Biology
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3010
>> dallas.warren at monash.edu
>> +61 3 9903 9304
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to resemble a nail.
>>
>>> -----Original Message-----
>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>>> bounces at gromacs.org] On Behalf Of Acoot Brett
>>> Sent: Saturday, 11 August 2012 9:59 AM
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] a residue move in extremely large scale in MD
>>>
>>> Dear Dr. Dallas Warren,
>>>
>>> My protein is a protein-peptide complex. The residues I mentioned which
>>> moves in a large scope is from the peptide, it is the last 3rd residue
>>> of the peptide, a lysine.
>>> I compared this lysine position with the other residue positions
>>> (including the peptide binding pocket and the all the peptide residues)
>>> with PDB from different time intervals (total MD is 10 ns, and I
>>> extracted the PDB every 0.5 ns, and then I align all the PDB files and
>>> compared the relative position of this lysine in different PDB files),
>>> I find this lysine position changed most significantly during the whole
>>> 10 ns MD.
>>>
>>> In addition, will you please tell me how to analysis whether the
>>> phenomenon is from periodid boundary effect? I have no knowledge on how
>>> boundary effect affect the MD.
>>>
>>> Cheers,
>>>
>>> Acoot
>>>
>>>
>>>
>>> ________________________________
>>> From: Dallas Warren <Dallas.Warren at monash.edu>
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Sent: Thursday, 9 August 2012 8:40 AM
>>> Subject: RE: [gmx-users] a residue move in extremely large scale in MD
>>>
>>> No, I can't, since you are the one with all the information in front of
>>> you, and I only have a couple of sentences filtered through you on what
>>> is going on.
>>>
>>> Some questions you can ask yourself to help answer the question you
>>> have:
>>>        And what did the residue do while you watched the trajectory?
>>>            Do you see it moving large distances?
>>>            What about the residues directly adjacent to it?
>>>        Where is it located within the protein?
>>>        How did you measure that the residue moved a large distance with
>>> the PDB files?
>>>            Just by looking at the coordinates?
>>>            Or did you use a script?
>>>
>>> In all likelihood what you are seeing here is simply a periodic
>>> boundary effect.  Which is why you should be actually watching the
>>> trajectory and what the residue itself does.  Seeing it with your eyes
>>> tells you what is going on much faster and it sinks in better too.
>>>
>>> Catch ya,
>>>
>>> Dr. Dallas Warren
>>> Drug Discovery Biology
>>> Monash Institute of Pharmaceutical Sciences, Monash University
>>> 381 Royal Parade, Parkville VIC 3010
>>> dallas.warren at monash.edu
>>> +61 3 9903 9304
>>> ---------------------------------
>>> When the only tool you own is a hammer, every problem begins to
>>> resemble a nail.
>>>
>>>
>>>> -----Original Message-----
>>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>>>> bounces at gromacs.org] On Behalf Of Acoot Brett
>>>> Sent: Wednesday, 8 August 2012 4:55 PM
>>>> To: Discussion list for GROMACS users
>>>> Subject: Re: [gmx-users] a residue move in extremely large scale in
>>> MD
>>>> Dear Catch ya,
>>>>
>>>> I have watched the trajectory of the simulation. Besdies, I got the
>>> PDb
>>>> file for the whole 10 ns MD every 500 ps. Then I compared all the PDB
>>>> files generated, and it confirms that 1 specific residues moves in an
>>>> extremely large space.
>>>>
>>>> Can you give me an explaination on it?
>>>>
>>>> Cheers,
>>>>
>>>> Acoot
>>>>
>>>>
>>>> ----- Original Message -----
>>>> From: Dallas Warren <Dallas.Warren at monash.edu>
>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>> Cc:
>>>> Sent: Wednesday, 8 August 2012 8:58 AM
>>>> Subject: RE: [gmx-users] a residue move in extremely large scale in
>>> MD
>>>> What information has "told you" that you have large scale movement?
>>>> Where did that information come from, how was it generated?  Have you
>>>> watch the trajectory of this simulation to see how the residue
>>> actually
>>>> moves?
>>>>
>>>> Catch ya,
>>>>
>>>> Dr. Dallas Warren
>>>> Drug Discovery Biology
>>>> Monash Institute of Pharmaceutical Sciences, Monash University
>>>> 381 Royal Parade, Parkville VIC 3010
>>>> dallas.warren at monash.edu
>>>> +61 3 9903 9304
>>>> ---------------------------------
>>>> When the only tool you own is a hammer, every problem begins to
>>>> resemble a nail.
>>>>
>>>>> -----Original Message-----
>>>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>>>>> bounces at gromacs.org] On Behalf Of Acoot Brett
>>>>> Sent: Wednesday, 8 August 2012 8:30 AM
>>>>> To: Discussion list for GROMACS users
>>>>> Subject: Re: [gmx-users] a residue move in extremely large scale in
>>>> MD
>>>>> Dear Marck,
>>>>>
>>>>> Will you please give me some suggestions on how to decide whether
>>> the
>>>>> probelm is from periodic boundary conditions?
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Acoot
>>>>>
>>>>>
>>>>> ----- Original Message -----
>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>>> Cc:
>>>>> Sent: Monday, 6 August 2012 10:31 PM
>>>>> Subject: Re: [gmx-users] a residue move in extremely large scale in
>>>> MD
>>>>> On 6/08/2012 8:58 PM, Acoot Brett wrote:
>>>>>>       Dear All,
>>>>>>
>>>>>> I have a protein with about 400 amino acids. I have done a
>>>> production
>>>>> MD of it. I find in the 400 amino acids, there is 1 amino acids,
>>>> during
>>>>> the whole MD process, this residue moves in a extremely large scope
>>>> in
>>>>> comparison with all the other residues.
>>>>>> Do you think this single residue with extremely large-scale
>>>> movement
>>>>> in the whole MD has important biological function, or has no
>>>> biological
>>>>> function?
>>>>>
>>>>> I'd start by proving that it was not a problem with periodic
>>> boundary
>>>>> conditions! If real, movement may or may not be indicative of
>>>>> functional significance - the question is impossible to answer out
>>> of
>>>>> context.
>>>>>
>>>>> Mark
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