[gmx-users] Amorphous polymer and periodic box

[mojtaba alaei]

Dear All

There are some initial steps for MD simulation of Amorphous polymer:

1-The periodic box,which is usually cubic are chosen

2-Then chain propagation takes place.As the chain propagates out of the 
periodic box through one face,it enters the box through the opposite 
face.Replication of the box thus produces correctly covalently connected 
chains.

therefore,I can't accommodate some chain polymer in a (periodicc )box 
completely.

Can gromacs do it(second step)?

Sincerely yours

Mojtaba



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