[gmx-users] Amorphous polymer and periodic box

[David]

On Sun, 2002-08-18 at 10:04, mojtaba alaei wrote:
> 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. .
Environment variable
> 
> 
> 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 
> chains.
> 
> therefore,I can't accommodate some chain polymer in a (periodic )box 
> completely.
> 
> Can gromacs do it(second step)?
> 
> 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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