Dear all
I want to simulate water diffusion in polymer matrix using Gromacs. I would like to know about system size effects. Then, I chose system with 10, 20 and 30 chains. In all systems, water content is invariant regarding to polymer chain ( 80 water molecule for each chain in all systems). When I did water cluster analysis(gmx clustsize), number of clusters was the same ( 3 for each system) and with increasing system size(number of chain and water with a constant ratio) I just saw an increase in size of each cluster ( 3 cluster in each system but with different sizes). Is it a true conclusion that with increase in system size and hence number of molucules we must expect for increase in cluster size not cluster numbers? is Cluster number fixed and could we correlate it to macroscopic sample?
Thank you
Mr. Rezayani,
In addition to the comment on posted by Mr. Zec, you should take into consideration the change of the macromolecular conformations of the matrix and the strength of hydrophobic interactions, therein; if any.
Please, consider reference [1]. Perhaps, it shall be useful to your study.
[1] International Journal of Biological Macromolecules 64 (2014) 383-391
Macromolecular ensembles of cyclodextrin crystallohydrates and clathrates – experimental and theoretical gas – and condense phase study
Bojidarka Ivanova, Michael Spiteller
> Is it a true conclusion that with increase in system size and hence number of
> molucules we must expect for increase in cluster size not cluster numbers?
No. One would expect exactly the opposite. The distribution of cluster sizes is fixed in the macroscopic system. By studying small simulation boxes you are trying to learn about this macroscopic distribution - the larger the box, the larger the cluster size you can access but also the longer it takes to simulate the clusters making and breaking in the simulation box. Make sure that you average cluster distribution over a long simulation time.
> is Cluster number fixed and could we correlate it to macroscopic sample?
No, the cluster number cannot be fixed. If you don't have single water molecules, doubles, triplets etc... You either have water concentration that is too high (check that the macroscopic system can actually contain this concentration of water) or your cut-off distance in the cluster identification is too large (decrease the cut-off distance to about the length of the hydrogen bond). It can also be a force field problem if the polymer model and the water model were developed independently and not together.
Dear Nebojša Zec
Thank you very much for your reply,
I used -cut 0.35 which was obtained from OW-OW of water molecules RDF. I tried different sizes from 10 chains to 60 chains. Number of clusters were constant from 10-30. But, after 30 chain (40,50 and 60) number of clusters increased from 3 to 10. I think it was a hint to increase system size.
Thank you again
Dear Bojidarka B. Ivanova
I increased system size and number of clusters changed. I think it was a hint to increase system size.
Thank you very much for your kind response
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