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Hi,<br><br>As I said, if you set a reference group (any name/group for pull_group0),<br>you apply a potential between two groups group0 and group1.<br>These two groups are treated completely equivalently (they both<br>experience the same force, but with opposite sign and they will both move<br>under influence of the force).<br><br>If you use an absolute reference (no name for pull_group0),<br>the reference is (0,0,0) plus pull_init. There is only pull group,<br>so only one group will move. But remember that the rest of the system<br>will move in the other direction if you remove COM motion.<br><br>Berk<br><br>> Date: Thu, 25 Jun 2009 14:08:48 +0200<br>> From: ilona.baldus@bioquant.uni-heidelberg.de<br>> To: gmx-users@gromacs.org<br>> Subject: RE: [gmx-users] pullx.xvg Meaning of output?<br>> <br>> What is meant by absolute reference? Can it be the Origin (0, 0, 0).<br>> Does it assume a random reference point for the pullx.xvg? I get a <br>> negative value for my first pulling group, even though it is inside <br>> the box and above the origin. Furthermore 0-Zcoord(pullgrp) doesn't <br>> fit either.<br>> Does it make any difference if I use reference_group = system or no <br>> reference group at all? Or what else do you usually use as a reference <br>> group? What does the reference group do during the simulation? I <br>> understand that pulling from both sides, Gromacs puts a spring at each <br>> pullgroup. Is there any restraint on the reference group?<br>> <br>> Cheers, Ilona<br>> <br>> <br>> <br>> Quoting Berk Hess <gmx3@hotmail.com>:<br>> <br>> ><br>> > Hi,<br>> ><br>> > In most cases you shoud NOT use an absolute reference.<br>> > In plain MD there is not absolute reference, therefore pulling<br>> > without a reference group is a recipe for trouble.<br>> > By default center of mass motion removal will be turned on,<br>> > in which case you are pulling against the center of mass of<br>> > the whole system. If you have solvent, thermodynamically<br>> > the pulling will have no effect, since the protein can move<br>> > along, if you pull slow enough. If you pull too fast (which is<br>> > very likely), you will get horrendous artifacts.<br>> ><br>> > Berk<br>> ><br>> >> Date: Thu, 25 Jun 2009 11:02:41 +0200<br>> >> From: ilona.baldus@bioquant.uni-heidelberg.de<br>> >> To: gmx3@hotmail.com<br>> >> Subject: RE: [gmx-users] pullx.xvg Meaning of output?<br>> >><br>> >><br>> >> Hi Berk,<br>> >><br>> >> I am trying to unfold a protein by stretching/pulling it from both<br>> >> sides in Z (and -Z) direction. To this end, I am trying to figure out<br>> >> the best parameters. If I understand you correctly, it should not make<br>> >> any difference to the pulling itself, i.e. the forces the protein<br>> >> experiences, whether a reference group is chosen or not.<br>> >> Unfortunately, my simulations show something different: I did exactly<br>> >> the same pulling simulation twice, using a backbone atom as reference<br>> >> group in the first case and no reference group in the second case. The<br>> >> differences I found are as follows:<br>> >> When I use no reference group, the molecule center moves less along<br>> >> the Z axis than in case of a defined reference group. The reason I do<br>> >> bother about that fact is that I do not want my molecule to leave the<br>> >> box on one end due to pulling effects even though the box is more than<br>> >> 3 nm longer than the unfolded protein.<br>> >> Also, pullf.xvg shows quite similar values for the simulation without<br>> >> reference group whereas forces differ more if a reference group is<br>> >> used. (see attached files). Why is that so?<br>> >><br>> >> Best wishes, Ilona<br>> >><br>> >><br>> >><br>> >><br>> >><br>> >> Quoting Berk Hess <gmx3@hotmail.com>:<br>> >><br>> >> ><br>> >> > Hi,<br>> >> ><br>> >> > Everything depends on what you want to accomplish, which you<br>> >> > do not write.<br>> >> > I don't see why you would want to look at single atoms.<br>> >> > Since you pull on COM's, only the COM coordinates are relevant.<br>> >> > If you want to look at single atoms, simply store them in the xtc file.<br>> >> ><br>> >> > If you have only two groups, there is no physical difference between<br>> >> > the reference group and the first pull group. They are simply two<br>> >> > groups between which the distance is calculated and the forces act.<br>> >> > If you used an absolute reference, 0Z is the absolute reference <br>> >> coordinate,<br>> >> > not the coordinate of a group.<br>> >> ><br>> >> > Berk<br>> >> ><br>> >> >> Date: Tue, 23 Jun 2009 14:39:48 +0200<br>> >> >> From: ilona.baldus@bioquant.uni-heidelberg.de<br>> >> >> To: gmx-users@gromacs.org<br>> >> >> Subject: RE: [gmx-users] pullx.xvg Meaning of output?<br>> >> >><br>> >> >><br>> >> >> Dear Berk,<br>> >> >><br>> >> >> Thanks for the quick reply. That leads me to my next questions:<br>> >> >> *I used the whole N and C residues for pulling. Is there any way of<br>> >> >> reconstructing the values for the single atoms? Or do you recommend<br>> >> >> only to pull N and C in the first place?<br>> >> >> *What does the reference group actually do? Can I simply leave it out?<br>> >> >> Does it influence pulling? What would be a good reference group? A<br>> >> >> random backbone atom from the middle of the protein?<br>> >> >><br>> >> >> I'm looking forward to your reply. Thank you very much in advance.<br>> >> >><br>> >> >> Best wishes, Ilona<br>> >> >><br>> >> >><br>> >> >> Quoting Berk Hess <gmx3@hotmail.com>:<br>> >> >><br>> >> >> ><br>> >> >> > Hi,<br>> >> >> ><br>> >> >> > This is actually not (yet) documented.<br>> >> >> > 0Z is the Z-coordinate of group 0.<br>> >> >> > 1dZ is the the Z-coordinate of group 1 minus the one of group 0.<br>> >> >> ><br>> >> >> > Berk<br>> >> >> ><br>> >> >> >> Date: Tue, 23 Jun 2009 12:54:37 +0200<br>> >> >> >> From: ilona.baldus@bioquant.uni-heidelberg.de<br>> >> >> >> To: gmx-users@gromacs.org<br>> >> >> >> Subject: [gmx-users] pullx.xvg Meaning of output?<br>> >> >> >><br>> >> >> >> Hi!<br>> >> >> >><br>> >> >> >> I am trying to understand the output of my pulling simulation:<br>> >> >> >> I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and<br>> >> >> >> -Z direction. I really cannot figure out the meaning of 1dZ and 2dZ.<br>> >> >> >> Since the website is down I cannot check on previous issues, so sorry<br>> >> >> >> for asking the same question again as I already asked last week but<br>> >> >> >> which remained unanswered.<br>> >> >> >><br>> >> >> >> I would appreciate any advice.<br>> >> >> >><br>> >> >> >> Thanks a lot. Ilona<br>> >> >> >> _______________________________________________<br>> >> >> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >> >> >> Please search the archive at http://www.gromacs.org/search<br>> >> >> before posting!<br>> >> >> >> Please don't post (un)subscribe requests to the list. Use the<br>> >> >> >> www interface or send it to gmx-users-request@gromacs.org.<br>> >> >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> >> >> ><br>> >> >> > _________________________________________________________________<br>> >> >> > Express yourself instantly with MSN Messenger! Download today <br>> >> it's FREE!<br>> >> >> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> >> >><br>> >> >><br>> >> >><br>> >> >> Ilona Baldus<br>> >> >> MPI Stuttgart<br>> >> >> INF 276<br>> >> >> 69120 Heidelberg<br>> >> >> Tel.: 06221-5451268<br>> >> >> _______________________________________________<br>> >> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >> >> Please search the archive at http://www.gromacs.org/search <br>> >> before posting!<br>> >> >> Please don't post (un)subscribe requests to the list. Use the<br>> >> >> www interface or send it to gmx-users-request@gromacs.org.<br>> >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> >> ><br>> >> > _________________________________________________________________<br>> >> > See all the ways you can stay connected to friends and family<br>> >> > http://www.microsoft.com/windows/windowslive/default.aspx<br>> >><br>> >><br>> >><br>> >> Ilona Baldus<br>> >> MPI Stuttgart<br>> >> INF 276<br>> >> 69120 Heidelberg<br>> >> Tel.: 06221-5451268<br>> ><br>> > _________________________________________________________________<br>> > Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> <br>> <br>> <br>> Ilona Baldus<br>> MPI Stuttgart<br>> INF 276<br>> 69120 Heidelberg<br>> Tel.: 06221-5451268<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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