[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Sep 8 16:09:50 CEST 2010


I highly doubt that you are correct. If you want more help, please  
copy and paste your commands and some relevant output back to the list.


--original message --

Message: 4
Date: Wed, 8 Sep 2010 15:07:15 +0200
From: maria goranovic <mariagoranovic at gmail.com>
Subject: Re: [gmx-users] restraining atoms to the plane at the bilayer
         center:        pull code ?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
         <aANLkTi=RQv+Ozsff0u5pMXsUAq-jpJaGhnNVpDrJM=ZY at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Chris,

Thank you for the code. I did check out pull_pbcatomN, and thank you for the
heads up that it is a global index. I used a central atom in the box for
each of the two groups as pull_pbcatom.

After using the code below with a rate constant of ~ 5500 for about 100 ps,
I realized that the atoms in different leaflets were being pulled in the
same direction.  I wanted certain atoms of either leaflet to be restrained
to the bilayer center. However, the code pulls all the atoms in the same
direction, such that atoms from one leaflet do approach the bilayer center,
but those from the other leaflet tend to get further away from the bilayer
center.  Thus, one actually needs two groups to be pulled, one each for the
atoms in each leaflet. Once this was fixed, the code worked just fine.

Again, thank you.


On Tue, Sep 7, 2010 at 3:40 PM, <chris.neale at utoronto.ca> wrote:

[Hide Quoted Text]
Maria, try this. There actually is a lot of this on the mailing list, so I
suggest checking it a little deeper for your next querry, or at least
outlining how you looked and what you found so that it is clear you have

Also, read about pull_pbcatomN and think carefully about how you want to
set that up. It is a *global* index.

pull                     = umbrella
pull_geometry            = position
pull_dim                 = N N Y
pull_start               = no
pull_nstxout             = 500
pull_nstfout             = 500
pull_ngroups             = 1
pull_group0              = <<<bilayer-group>>>
pull_pbcatom0            = 0
pull_group1              = <<<pulled-group>>>
pull_pbcatom1            = 0
pull_init1               = 0 0 0.0
pull_rate1               = 0
pull_k1                  = <<<force-constant>>>
pull_vec1                = 0 0 0

-- original message --

The manual does discuss restraining to a plane, but this must be the plane
in which the atom is already present.

[  position_restraints ]
; ai   funct    fc
3   1   1000   0   0

How about restraining the atom to some other plane? For example, how about
restraining a phosphate group initially at the lipid-water interface to the
bilayer center (for whatever fancy reasons) ? Won't this require pulling
atom to that plane first?

If it can be achieved using the position restraints alone, it is not clear
to me how to do this?


On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul <jalemkul at vt.edu>

maria goranovic wrote:

   I want to restrain certain atoms of my simulation to the plane
perpendicular to the bilayer normal, and at the bilayer center. Can
please provide a quick guide on how to do this? I read the pull-code
options, but restraining to a plane did not seem possible?

   You can restrain atoms to a plane using position restraints.  See the
manual for an example.
Maria G.
Technical University of Denmark

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