[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

[maria goranovic]

Well, Xavier :). I will give it one more shot, and get back to the list next
week !

On Fri, Nov 6, 2009 at 4:45 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
>  Well .. I mean .. the lipids are not put back into the central simulation
>> cell in the xy plane. so they keep the nojump effect
>>
> Ok, what you describe does not make sense, not that you do not make
> sense but the fact that the lipids dot not come back to the central cell
> in the xy plan does not make sense!
> I really do not see why that could be! Never seen it ...
>
> In most cases for membrane proteins the problem of cutting molecules
> comes from the xy plan not the z direction.
>
> If I were you I would check for a last time your tpr file to make sure it
> is
> indeed what you think it is and it is fine ... erase all files and redo the
> all process, something went bad at some point.
>
>
>> what do you mean "expand"? They do not get back in the box meaning they
>> keep the nojump
>> effect or it is just that they have the tail out of the box?
>> -pbc mol will put the COM of the molecule (protein/lipid/water ...) in the
>> box and leave the molecule
>> as a whole (no cutting bonds).
>>
>>
>> Well you can see the bilayer as protein complex where each monomer is
>> a leaflet. Applying -pbc nojump on the trajectory would simply keep the
>> two
>> leaflets together. Then the system can be centered using the bilayer as
>> reference: this would put the bilayer at the center of the z axis. The
>> movements
>> "out of the box" can then be corrected using -pbc mol.
>> It is trivial is the reference structures are correct.
>>
>> I do not think this is the case. In a protein complex, each monomer is
>> bonded to the next amino acid, and therefore -pbc mol works, because the
>> entire protein is a single molecule . In lipids however, why would trjconv
>> treat the leaflet as a monomer?
>>
>> -pbc mol will work on each molecule, see above, but not on the lipid
>> bilayer of course.
>> This is why you use nojump first! and then center ... then the lipid
>> molecules will be put
>> in the box on the xy plan but not across the z axis
>>
>> And -pbc nojump will also work on each molecule, not on a leaflet as a
>> whole.
>>
>> I think the following takes place:
>>
>> The bilayer moves along -z, and some lipids eventually leave the box on
>> one edge, and appear on the other edge.  -pbc nojump ensures that the lipids
>> do not do this, and instead continue drifting along -z. thus the center of
>> mass of the lipids should just keep moving along -z after using -pbc nojump.
>> It is therefore easy to correct this drift while using -center.
>>
>> However, the lipids also diffuse in the x and the y direction, but this
>> diffusion is random. THIS TOO, is changed by using -pbc nojump. Thus, pbc
>> nojump changes the center of mass behavior of the lipids in all three
>> directions. It can be corrected for z, because the z-drift is always along
>> one direction (all lipids diffuse either in -z or +z), but cannot be
>> corrected for xy, because individual lipids diffuse randomly (both along
>> +x/y or -x/y)
>>
>> _______________________________________________
>> 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/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> _______________________________________________
> 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/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/mailing_lists/users.php
>



-- 
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/20091106/a2776426/attachment.html>