[gmx-users] pullx.xvg Meaning of output?

Berk Hess gmx3 at hotmail.com
Thu Jun 25 15:54:39 CEST 2009 

Hi,

As I said, if you set a reference group (any name/group for pull_group0),
you apply a potential between two groups group0 and group1.
These two groups are treated completely equivalently (they both
experience the same force, but with opposite sign and they will both move
under influence of the force).

If you use an absolute reference (no name for pull_group0),
the reference is (0,0,0) plus pull_init. There is only pull group,
so only one group will move. But remember that the rest of the system
will move in the other direction if you remove COM motion.

Berk

> Date: Thu, 25 Jun 2009 14:08:48 +0200
> From: ilona.baldus at bioquant.uni-heidelberg.de
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] pullx.xvg  Meaning of output?
> 
> What is meant by absolute reference? Can it be the Origin (0, 0, 0).
> Does it assume a random reference point for the pullx.xvg? I get a  
> negative value for my first pulling group, even though it is inside  
> the box and above the origin. Furthermore 0-Zcoord(pullgrp) doesn't  
> fit either.
> Does it make any difference if I use reference_group = system or no  
> reference group at all? Or what else do you usually use as a reference  
> group? What does the reference group do during the simulation? I  
> understand that pulling from both sides, Gromacs puts a spring at each  
> pullgroup. Is there any restraint on the reference group?
> 
> Cheers, Ilona
> 
> 
> 
> Quoting Berk Hess <gmx3 at hotmail.com>:
> 
> >
> > Hi,
> >
> > In most cases you shoud NOT use an absolute reference.
> > In plain MD there is not absolute reference, therefore pulling
> > without a reference group is a recipe for trouble.
> > By default center of mass motion removal will be turned on,
> > in which case you are pulling against the center of mass of
> > the whole system. If you have solvent, thermodynamically
> > the pulling will have no effect, since the protein can move
> > along, if you pull slow enough. If you pull too fast (which is
> > very likely), you will get horrendous artifacts.
> >
> > Berk
> >
> >> Date: Thu, 25 Jun 2009 11:02:41 +0200
> >> From: ilona.baldus at bioquant.uni-heidelberg.de
> >> To: gmx3 at hotmail.com
> >> Subject: RE: [gmx-users] pullx.xvg  Meaning of output?
> >>
> >>
> >> Hi Berk,
> >>
> >> I am trying to unfold a protein by stretching/pulling it from both
> >> sides in Z (and -Z) direction. To this end, I am trying to figure out
> >> the best parameters. If I understand you correctly, it should not make
> >> any difference to the pulling itself, i.e. the forces the protein
> >> experiences, whether a reference group is chosen or not.
> >> Unfortunately, my simulations show something different: I did exactly
> >> the same pulling simulation twice, using a backbone atom as reference
> >> group in the first case and no reference group in the second case. The
> >> differences I found are as follows:
> >> When I use no reference group, the molecule center moves less along
> >> the Z axis than in case of a defined reference group. The reason I do
> >> bother about that fact is that  I do not want my molecule to leave the
> >> box on one end due to pulling effects even though the box is more than
> >> 3 nm longer than the unfolded protein.
> >> Also, pullf.xvg shows quite similar values for the simulation without
> >> reference group whereas forces differ more if a reference group is
> >> used. (see attached files). Why is that so?
> >>
> >> Best wishes, Ilona
> >>
> >>
> >>
> >>
> >>
> >> Quoting Berk Hess <gmx3 at hotmail.com>:
> >>
> >> >
> >> > Hi,
> >> >
> >> > Everything depends on what you want to accomplish, which you
> >> > do not write.
> >> > I don't see why you would want to look at single atoms.
> >> > Since you pull on COM's, only the COM coordinates are relevant.
> >> > If you want to look at single atoms, simply store them in the xtc file.
> >> >
> >> > If you have only two groups, there is no physical difference between
> >> > the reference group and  the first pull group. They are simply two
> >> > groups between which the distance is calculated and the forces act.
> >> > If you used an absolute reference, 0Z is the absolute reference   
> >> coordinate,
> >> > not the coordinate of a group.
> >> >
> >> > Berk
> >> >
> >> >> Date: Tue, 23 Jun 2009 14:39:48 +0200
> >> >> From: ilona.baldus at bioquant.uni-heidelberg.de
> >> >> To: gmx-users at gromacs.org
> >> >> Subject: RE: [gmx-users] pullx.xvg  Meaning of output?
> >> >>
> >> >>
> >> >> Dear Berk,
> >> >>
> >> >> Thanks for the quick reply. That leads me to my next questions:
> >> >> *I used the whole N and C residues for pulling. Is there any way of
> >> >> reconstructing the values for the single atoms? Or do you recommend
> >> >> only to pull N and C in the first place?
> >> >> *What does the reference group actually do? Can I simply leave it out?
> >> >> Does it influence pulling?  What would be a good reference group? A
> >> >> random backbone atom from the middle of the protein?
> >> >>
> >> >> I'm looking forward to your reply. Thank you very much in advance.
> >> >>
> >> >> Best wishes, Ilona
> >> >>
> >> >>
> >> >> Quoting Berk Hess <gmx3 at hotmail.com>:
> >> >>
> >> >> >
> >> >> > Hi,
> >> >> >
> >> >> > This is actually not (yet) documented.
> >> >> > 0Z is the Z-coordinate of group 0.
> >> >> > 1dZ is the the Z-coordinate of group 1 minus the one of group 0.
> >> >> >
> >> >> > Berk
> >> >> >
> >> >> >> Date: Tue, 23 Jun 2009 12:54:37 +0200
> >> >> >> From: ilona.baldus at bioquant.uni-heidelberg.de
> >> >> >> To: gmx-users at gromacs.org
> >> >> >> Subject: [gmx-users] pullx.xvg  Meaning of output?
> >> >> >>
> >> >> >> Hi!
> >> >> >>
> >> >> >> I am trying to understand the output of my pulling simulation:
> >> >> >> I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and
> >> >> >> -Z direction. I really cannot figure out the meaning of 1dZ and 2dZ.
> >> >> >> Since the website is down I cannot check on previous issues, so sorry
> >> >> >> for asking the same question again as I already asked last week but
> >> >> >> which remained unanswered.
> >> >> >>
> >> >> >> I would appreciate any advice.
> >> >> >>
> >> >> >> Thanks a lot. Ilona
> >> >> >> _______________________________________________
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> >> >>
> >> >> Ilona Baldus
> >> >> MPI Stuttgart
> >> >> INF 276
> >> >> 69120 Heidelberg
> >> >> Tel.: 06221-5451268
> >> >> _______________________________________________
> >> >> gmx-users mailing list    gmx-users at gromacs.org
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> >>
> >>
> >> Ilona Baldus
> >> MPI Stuttgart
> >> INF 276
> >> 69120 Heidelberg
> >> Tel.: 06221-5451268
> >
> > _________________________________________________________________
> > Express yourself instantly with MSN Messenger! Download today it's FREE!
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> 
> 
> 
> Ilona Baldus
> MPI Stuttgart
> INF 276
> 69120 Heidelberg
> Tel.: 06221-5451268
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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