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

[maria goranovic]

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.

Maria



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

> 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
> tried.
>
> Also, read about pull_pbcatomN and think carefully about how you want to
> set that up. It is a *global* index.
>
> ; COM PULLING
> 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
> the
> 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?
>
> -Maria
>
>
>
> On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul <jalemkul at vt.edu>
> wrote:
>
>
>>
>> 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
>>> someone
>>> 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.
>>
>> -Justin
>>
>>
>>
>>
>>> --
>>> Maria G.
>>> Technical University of Denmark
>>> Copenhagen
>>>
>>>
>>>
>
> --
> 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/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100908/fffd856b/attachment.html>