[gmx-users] Amorphous polymer and periodic box

mojtaba alaei mo_alaei at hotmail.com
Sun Aug 18 10:04:28 CEST 2002

Dear All

Dr.spoel wrote at 17 Aug 2002 11:10:08:
>If you do not have an infinite molecule it is usually fine, as long as
>your molecule is shorter than 3 box lengths, otherwise the same env.
>var. has to be set.

I don't understand words env. and var. .

I wrote at Sat, 17 Aug 2002 08:57:49 :

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 

therefore,I can't accommodate some chain polymer in a (periodic )box 

Can gromacs do it(second step)?

Sincerely yours


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