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Hi,<br><br>The suggested pull parameters below are correct,<br>except that you should not use pull_geometry=position,<br>since that will only make group1 move, not group0.<br>You should use pull_geometry=distance,<br>pull_vec1 is that no longer required, since distance<br>will move the two groups away along the vector<br>between the two COM's.<br><br>Berk<br><br>> Date: Fri, 31 Jul 2009 09:58:56 +0200<br>> From: schlesi@uni-mainz.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Re: Pulling a CG protein<br>> <br>> Hi Johnny,<br>> i replied something to the pull-code of your question. But problem was,<br>> i didn't edited the subject line...<br>> So here is my answer (see below) with the right subject line (so that<br>> you hopefully find it).<br>> Hope it helps you.<br>> Thomas<br>> <br>> > <br>> > Message: 3<br>> > Date: Thu, 30 Jul 2009 12:08:40 -0700 (PDT)<br>> > From: "Johnny Lam" <johntus@berkeley.edu><br>> > Subject: Re: [gmx-users] Pulling a CG protein<br>> > To: gmx-users@gromacs.org<br>> > Cc: baaden@smplinux.de<br>> > Message-ID:<br>> > <56441.128.32.142.53.1248980920.squirrel@calmail.berkeley.edu><br>> > Content-Type: text/plain;charset=iso-8859-1<br>> > <br>> > Hi XAvier, Marc, and David,<br>> > <br>> > Thank you so much for the reply and encouragement ;-). Please forgive me<br>> > as I am trying to learn how to reply to the thread that I started. With<br>> > regards to the fun discussion, it was my original intent to compare the<br>> > results of pulling with the MARTINI forcefield (if the pull code was<br>> > correct) with already published works on MD (using all-atomistic modeling<br>> > of course :-)). I just wanted to know whether the pull code that I am<br>> > using will be valid at all. If you guys can verify that would be awesome!<br>> > Otherwise, I'd be happy to share the results with you guys if you wish.<br>> > Again, thanks!<br>> > <br>> > --Johnny<br>> > <br>> > <br>> > -------------------------------------------------<br>> > Johnny Lam<br>> > ISPE Berkeley Chapter External Vice President<br>> > Department of Bioengineering<br>> > College of Engineering<br>> > University of California, Berkeley<br>> > Tel: (408) 655- 6829<br>> > Email: johntus@berkeley.edu<br>> > <br>> > <br>> > ----------------------------------------------------------------------<br>> > ><br>> > > Message: 1<br>> > > Date: Wed, 29 Jul 2009 16:04:54 -0700 (PDT)<br>> > > From: "Johnny Lam" <johntus@berkeley.edu><br>> > > Subject: [gmx-users] Pulling a CG protein<br>> > > To: gmx-users@gromacs.org<br>> > > Message-ID:<br>> > > <55658.128.32.142.63.1248908694.squirrel@calmail.berkeley.edu><br>> > > Content-Type: text/plain;charset=iso-8859-1<br>> > ><br>> > > Dear gromacs users,<br>> > ><br>> > > Hi, I am trying to pull apart a relatively large protein (CG using the<br>> > > martini force field) by pulling on two groups in opposite directions. To<br>> > > do this, I will be using the following .mdp file. However, I am almost<br>> > > certain that it contains errors:<br>> > ><br>> <br>> -snip<br>> <br>> > ><br>> > > ; Pulling<br>> > > pull = afm<br>> > > pull_geometry = direction<br>> > > pull_start = no<br>> > > pull_nstxout = 10<br>> > > pull_nstfout = 10<br>> > > pull_ngroups = 2<br>> > > pull_group0 =<br>> > > pull_group1 = pull<br>> > > pull_vec1 = -0.1764 -0.9823 -0.0625<br>> > > pull_init1 = -0.1764 -0.9823 -0.0625<br>> > > pull_rate1 = 0.0001<br>> > > pull_k1 = 1000<br>> > > pull_group2 = freeze<br>> > > pull_vec2 = 0.1764 0.9823 0.0625<br>> > > pull_init2 = 0.1764 0.9823 0.0625<br>> > > pull_rate2 = 0.0000000001<br>> > > pull_k2 = 5000<br>> > ><br>> > ><br>> <br>> Think the first problem is the:<br>> pull = afm<br>> In the manual there is no more a 'afm' option, but as far as i know<br>> 'umbrella' should be the same (don't ask me why there was no error<br>> message about this). If you have no pull_group0 you could get problem<br>> with the com-motion.<br>> If you want to pull 'pull' away from 'freeze', i would do the following:<br>> <br>> pull = umbrella<br>> pull_geometry = position<br>> pull_start = yes (we don't want to calculate the initial distance<br>> between 'pull' and 'freeze' by hand)<br>> pull_ngroups = 1 (because the reference group doesn't count to this value)<br>> pull_dim = Y Y Y (because we want to pull in 3D)<br>> pull_group0 = freeze<br>> pull_group1 = pull<br>> pull_vec1 = vector from 'freeze' to 'pull'<br>> pull_init1 = 0.0 0.0 0.0<br>> <br>> Now you are pulling 'pull' away from 'freeze' and and you should have no<br>> problem with com-motion.<br>> If you want to fix the position of 'freeze' i would use position_restraints.<br>> One thing: once i had problems with the 'pull_weightsX', i got (with one<br>> system) every time error messages (i had only 1atom in each group and<br>> tried the values 0 and 1 both, but didn't work). So i left these to<br>> values blank and GROMACS selected them, and it worked. In other<br>> simulations with a similar setup i had no problems with 'pull_weightsX'.<br>> <br>> <br>> > > The reason why group 2 has such a high force constant and low pull<br>> rate is<br>> > > because I wanted to simulate putting a harmonic constraint on the freeze<br>> > > group. However, when I process this .mdp with grompp, I get the<br>> following<br>> > > message:<br>> > ><br>> > > WARNING 1 [file md_vinculin.mdp, line unknown]:<br>> > > Unknown or double left-hand 'pull_group2' in parameter file<br>> <br>> Another thing could be that you have no index group with the name 'freeze'?<br>> <br>> But best have also a look in the new (GROMACS 4) manual. COM pulling is<br>> described from page 156 on.<br>> <br>> Hope this helps<br>> Thomas<br>> <br>> > ><br>> > ><br>> > ><br>> > > WARNING 2 [file md_vinculin.mdp, line unknown]:<br>> > > Unknown or double left-hand 'pull_vec2' in parameter file<br>> > ><br>> > ><br>> > > The version of gromacs I have running on my powerpc is 4.0.5 so the pull<br>> > > code should be implemented in the .mdp file. I am not sure if I<br>> specified<br>> > > the parameters correctly. Please help! Thanks!<br>> > ><br>> > > --Johnny<br>> > ><br>> > > -------------------------------------------------<br>> > > Johnny Lam<br>> > > ISPE Berkeley Chapter External Vice President<br>> > > Department of Bioengineering<br>> > > College of Engineering<br>> > > University of California, Berkeley<br>> > > Tel: (408) 655- 6829<br>> > > Email: johntus@berkeley.edu<br>> > ><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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