[gmx-users] Peptide aggregation

[Léon Salgado]

Dear Dr. Ran Friedman

Would you please be so kind to send me your version, to calculate then 
the rgyr "of the largest aggregate".
The box was built with a layer of 1.2 nm around the solute (editconf -d 
1.2).

Leon

Ran Friedman wrote:
> Dear Leon,
>
> You can try to use g_clustsize to get the aggregates. I have a version
> that can calculate the gyration radius of the largest aggregate, but
> this would work only if your box is big enough and I haven't tried it
> with rhombic dodecahedron boxes.
>
> Ran.
>
> Léon Salgado wrote:
>   
>> Dear gmx users
>>
>> I did some simulations of multimers (peptides) in rhombic dodecahedron
>> boxes. In the initial configuration of the system, the peptides are
>> close of each other in the center of the box.
>>
>> My aim to see if the peptides do aggregate during the trajectory or if
>> they tend to stay apart. A rough estimate can be taken from the
>> gyration radius for all the peptides together.
>>
>> Already did a trjconv -pbc nojump pre-treatment on the trajectory,
>> before calculating the Rgyr. The gyration.xvg plots sometimes do show
>> abrupt jumps, and this is surely due to boundary effects, if I
>> correctly understood the PBC idea. If a peptide approaches the
>> boundary, it appears on the opposite side, thus rgyr will show a false
>> sudden increase. In fact, the peptide could be closer to the rest of
>> the other peptide molecule(s).
>>
>> Thus my question is:
>> how to deal with peptide clusters that span over the periodic boundaries?
>>
>> A similar question was done by Singh:
>> http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html
>>
>> and it  was suggested by Chris Neale to pre-process the trajectory
>> (see
>> http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html)
>> with:
>>
>> trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
>> grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
>> trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
>>
>> but I'm getting infinite loops on the -pbc cluster treatment, same as
>> reported by Chris
>> (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html).
>>
>> Best,
>> Léon
>>
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>>     
>
>
>