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.war...@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-boun...@gromacs.org [mailto:gmx-users- > boun...@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.abra...@anu.edu.au> > To: Discussion list for GROMACS users <gmx-users@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.war...@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-boun...@gromacs.org [mailto:gmx-users- > >> boun...@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.war...@monash.edu> > >> To: Discussion list for GROMACS users <gmx-users@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.war...@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-boun...@gromacs.org [mailto:gmx-users- > >>> boun...@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.war...@monash.edu> > >>> To: Discussion list for GROMACS users <gmx-users@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.war...@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-boun...@gromacs.org [mailto:gmx-users- > >>>> boun...@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.abra...@anu.edu.au> > >>>> To: Discussion list for GROMACS users <gmx-users@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 > >>>> -- gmx-users mailing list gmx-users@gromacs.org > >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>>> * Only plain text messages are allowed! > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > >>>> * Please don't post (un)subscribe requests to the list. Use the > www > >>>> interface or send it to gmx-users-requ...@gromacs.org. > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> -- > >>>> gmx-users mailing list gmx-users@gromacs.org > >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>>> * Only plain text messages are allowed! > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > >>>> * Please don't post (un)subscribe requests to the list. Use the > >>>> www interface or send it to gmx-users-requ...@gromacs.org. > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> -- > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> * Only plain text messages are allowed! > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> * Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to gmx-users-requ...@gromacs.org. > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> -- > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> * Only plain text messages are allowed! > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> * Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to gmx-users-requ...@gromacs.org. > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Only plain text messages are allowed! > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Only plain text messages are allowed! > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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