[gmx-users] Re: Pulling a CG protein
Berk Hess
gmx3 at hotmail.com
Fri Jul 31 10:11:50 CEST 2009
Hi,
The suggested pull parameters below are correct,
except that you should not use pull_geometry=position,
since that will only make group1 move, not group0.
You should use pull_geometry=distance,
pull_vec1 is that no longer required, since distance
will move the two groups away along the vector
between the two COM's.
Berk
> Date: Fri, 31 Jul 2009 09:58:56 +0200
> From: schlesi at uni-mainz.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: Pulling a CG protein
>
> Hi Johnny,
> i replied something to the pull-code of your question. But problem was,
> i didn't edited the subject line...
> So here is my answer (see below) with the right subject line (so that
> you hopefully find it).
> Hope it helps you.
> Thomas
>
> >
> > Message: 3
> > Date: Thu, 30 Jul 2009 12:08:40 -0700 (PDT)
> > From: "Johnny Lam" <johntus at berkeley.edu>
> > Subject: Re: [gmx-users] Pulling a CG protein
> > To: gmx-users at gromacs.org
> > Cc: baaden at smplinux.de
> > Message-ID:
> > <56441.128.32.142.53.1248980920.squirrel at calmail.berkeley.edu>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > Hi XAvier, Marc, and David,
> >
> > Thank you so much for the reply and encouragement ;-). Please forgive me
> > as I am trying to learn how to reply to the thread that I started. With
> > regards to the fun discussion, it was my original intent to compare the
> > results of pulling with the MARTINI forcefield (if the pull code was
> > correct) with already published works on MD (using all-atomistic modeling
> > of course :-)). I just wanted to know whether the pull code that I am
> > using will be valid at all. If you guys can verify that would be awesome!
> > Otherwise, I'd be happy to share the results with you guys if you wish.
> > Again, thanks!
> >
> > --Johnny
> >
> >
> > -------------------------------------------------
> > Johnny Lam
> > ISPE Berkeley Chapter External Vice President
> > Department of Bioengineering
> > College of Engineering
> > University of California, Berkeley
> > Tel: (408) 655- 6829
> > Email: johntus at berkeley.edu
> >
> >
> > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Wed, 29 Jul 2009 16:04:54 -0700 (PDT)
> > > From: "Johnny Lam" <johntus at berkeley.edu>
> > > Subject: [gmx-users] Pulling a CG protein
> > > To: gmx-users at gromacs.org
> > > Message-ID:
> > > <55658.128.32.142.63.1248908694.squirrel at calmail.berkeley.edu>
> > > Content-Type: text/plain;charset=iso-8859-1
> > >
> > > Dear gromacs users,
> > >
> > > Hi, I am trying to pull apart a relatively large protein (CG using the
> > > martini force field) by pulling on two groups in opposite directions. To
> > > do this, I will be using the following .mdp file. However, I am almost
> > > certain that it contains errors:
> > >
>
> -snip
>
> > >
> > > ; Pulling
> > > pull = afm
> > > pull_geometry = direction
> > > pull_start = no
> > > pull_nstxout = 10
> > > pull_nstfout = 10
> > > pull_ngroups = 2
> > > pull_group0 =
> > > pull_group1 = pull
> > > pull_vec1 = -0.1764 -0.9823 -0.0625
> > > pull_init1 = -0.1764 -0.9823 -0.0625
> > > pull_rate1 = 0.0001
> > > pull_k1 = 1000
> > > pull_group2 = freeze
> > > pull_vec2 = 0.1764 0.9823 0.0625
> > > pull_init2 = 0.1764 0.9823 0.0625
> > > pull_rate2 = 0.0000000001
> > > pull_k2 = 5000
> > >
> > >
>
> Think the first problem is the:
> pull = afm
> In the manual there is no more a 'afm' option, but as far as i know
> 'umbrella' should be the same (don't ask me why there was no error
> message about this). If you have no pull_group0 you could get problem
> with the com-motion.
> If you want to pull 'pull' away from 'freeze', i would do the following:
>
> pull = umbrella
> pull_geometry = position
> pull_start = yes (we don't want to calculate the initial distance
> between 'pull' and 'freeze' by hand)
> pull_ngroups = 1 (because the reference group doesn't count to this value)
> pull_dim = Y Y Y (because we want to pull in 3D)
> pull_group0 = freeze
> pull_group1 = pull
> pull_vec1 = vector from 'freeze' to 'pull'
> pull_init1 = 0.0 0.0 0.0
>
> Now you are pulling 'pull' away from 'freeze' and and you should have no
> problem with com-motion.
> If you want to fix the position of 'freeze' i would use position_restraints.
> One thing: once i had problems with the 'pull_weightsX', i got (with one
> system) every time error messages (i had only 1atom in each group and
> tried the values 0 and 1 both, but didn't work). So i left these to
> values blank and GROMACS selected them, and it worked. In other
> simulations with a similar setup i had no problems with 'pull_weightsX'.
>
>
> > > The reason why group 2 has such a high force constant and low pull
> rate is
> > > because I wanted to simulate putting a harmonic constraint on the freeze
> > > group. However, when I process this .mdp with grompp, I get the
> following
> > > message:
> > >
> > > WARNING 1 [file md_vinculin.mdp, line unknown]:
> > > Unknown or double left-hand 'pull_group2' in parameter file
>
> Another thing could be that you have no index group with the name 'freeze'?
>
> But best have also a look in the new (GROMACS 4) manual. COM pulling is
> described from page 156 on.
>
> Hope this helps
> Thomas
>
> > >
> > >
> > >
> > > WARNING 2 [file md_vinculin.mdp, line unknown]:
> > > Unknown or double left-hand 'pull_vec2' in parameter file
> > >
> > >
> > > The version of gromacs I have running on my powerpc is 4.0.5 so the pull
> > > code should be implemented in the .mdp file. I am not sure if I
> specified
> > > the parameters correctly. Please help! Thanks!
> > >
> > > --Johnny
> > >
> > > -------------------------------------------------
> > > Johnny Lam
> > > ISPE Berkeley Chapter External Vice President
> > > Department of Bioengineering
> > > College of Engineering
> > > University of California, Berkeley
> > > Tel: (408) 655- 6829
> > > Email: johntus at berkeley.edu
> > >
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