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

Dallas Warren Dallas.Warren at monash.edu
Wed Aug 15 00:25:39 CEST 2012 

You are missing a major conceptual principle of MD here.

See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Read manual, section 3.2

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: Tuesday, 14 August 2012 5:54 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] a residue move in extremely large scale in MD
> 
> 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?
> 
> 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.
> 
> 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_Cond
> itions
> 
> 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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