[gmx-users] Amorphous polymer and periodic box

David spoel at xray.bmc.uu.se
Sat Aug 17 11:10:08 CEST 2002

On Sat, 2002-08-17 at 10:57, mojtaba alaei wrote:
> 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)?
If I understand you correctly you want to have an infinite molecule. Is
that correct? This can be done, but you have to set an environment
variable to tell GROMACS that you want to do the full periodic bundary
calculations (as opposed to our optimized scheme).

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.
> Sincerely yours
> Mojtaba
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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