[gmx-users] Peptide aggregation

[Ran Friedman, Biochemisches Inst.]

Dear Leon,

Note that you can already use g_clustsize to check the aggregates. I'll 
contact you off list next week with the modified version.

Ran

On Fri, 19 Sep 2008 17:13:02 +0100
  Léon Salgado <leon.salgado at gmail.com> wrote:
> 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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>>>     
>>
>>
>>   
> 
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------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Institute of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Skype: ran.friedman
------------------------------------------------------