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

[maria goranovic]

I will try centering with one of the lipid tail atoms .. that could solve
the problem.

This the way I have specified the comm_groups:

nstcomm = 1
comm-grps = Lipid W

OR

nstcom = 1
comm-grps = system

-Maria

On Wed, Sep 2, 2009 at 4:04 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> I am not sure how to fix the trajectory that has drifted ...
>
> But if your bilayer drifts even if you use a removal of the COM for the
> water and
> bilayer separately that means there is problem in the code! And this should
> be
> fixed.
>
> XAvier.
>
>
> On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:
>
>  Dear Experts
>>
>> I had posted this earlier, but the problem was not solved by earlier
>> suggestions. So am posting again.
>>
>> I am simulating a POPC bilayer using MARTINI. The simulation ran fine, but
>> the bilayer drifted towards the edge of the box along the bilayer normal,
>> and eventually some of the atoms crossed the box boundaries. In some cases,
>> entire lipid molecules crossed the box boundaries. I tried to recenter the
>> trajectory, so that the lipid bilayer would be at the center of the box at
>> all times. But for some reason, this does not seem to work? I have tried
>> simulations using a single comm_group for the entire system, as well as
>> separate ones for the lipid and water, but the same problem appears in
>> either case.
>>
>> Typically, for all-atom bilayers, the following set of commands works to
>> correct the drift:
>>
>> #### first convert original trajectory to a temp. xtc ###
>> echo  3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center -boxcenter
>> zero -pbc mol -n popc.ndx
>> #### then convert temp.xtc to the final trajecory ###
>> echo  3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc  -center -boxcenter
>> zero  -pbc mol -n popc.ndx
>>
>> where groups 3 and 0 are the lipid and the whole system respectively, and
>> final.xtc is my final trajectory.
>>
>> However, this does not work for the MARTINI systems. Looking at the final
>> trajectory in VMD, the bilayer is either at the center of the box, or it is
>> split at the box edges, with each monomer being in different leaflets.
>>
>> If I plot the center of mass motion of the entire system in the original
>> trajectory .. the system seems to drift by ~ 2-3 angstroms in one direction.
>> As a result, water center of mass drifts in the opposite direction (because
>> of PBC).
>>
>> Are there any suggestions to sort this out? One option is  to write the
>> entire trajectory to .gro files, recenter all of them (depending upon
>> whether the bilayer is in the center or is split at the box edge), and
>> concatenate the gro files again.but this is tedious, even if scripted.
>>
>> Please let me know if i can provide any additional info ?
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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