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

Thu Jun 25 14:08:48 CEST 2009

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
>> >> >> _______________________________________________
>> >> >> gmx-users mailing list    gmx-users at gromacs.org
>> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> >> Please search the archive at http://www.gromacs.org/search
>> >> before posting!
>> >> >> Please don't post (un)subscribe requests to the list. Use the
>> >> >> www interface or send it to gmx-users-request at gromacs.org.
>> >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >> >
>> >> > _________________________________________________________________
>> >> > Express yourself instantly with MSN Messenger! Download today   
>> it's FREE!
>> >> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>> >>
>> >>
>> >>
>> >> 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
>> >> Please search the archive at http://www.gromacs.org/search   
>> before posting!
>> >> Please don't post (un)subscribe requests to the list. Use the
>> >> www interface or send it to gmx-users-request at gromacs.org.
>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>> > _________________________________________________________________
>> > See all the ways you can stay connected to friends and family
>> > http://www.microsoft.com/windows/windowslive/default.aspx
>>
>>
>>
>> Ilona Baldus
>> MPI Stuttgart
>> INF 276
>> 69120 Heidelberg
>> Tel.: 06221-5451268
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE!
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/

Ilona Baldus
MPI Stuttgart
INF 276
69120 Heidelberg
Tel.: 06221-5451268