[gmx-users] periodic condition for a hexagonal prism

[Tsjerk Wassenaar]

Hi Yuguang,

To obtain a hexagonal prism, use editconf with option -angles 60 90 90 and 
vector lengths appropriate for your system. I assume you will use it for an 
infinite DNA strand? Otherwise it may give trouble with rotations, unless 
you use a rotational constraint algorithm.

Cheers,

Tsjerk

On 9/16/05, Mu Yuguang (Dr) <YGMu at ntu.edu.sg> wrote:
> 
> Dear All,
> Is there a way to use hexagonal prism condition (good for DNA fiber) in
> gromacs ?
> 
> Dr. Yuguang Mu
> Division of Structural and Computational Biology
> School of Biological Sciences
> Nanyang Technological University
> 60 Nanyang Drive
> Singapore 637551
> Tel: 63162885
> Fax: 67913856
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
> Sent: Friday, September 16, 2005 12:33 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] box type in gro file
> 
> > In gro file the last line gives the information of periodic box.
> Besides
> > first three numbers of a,b,c, what other numbers mean?
> 
> See http://www.gromacs.org/documentation/reference_3.2/online/files.html
> 
> They give the vectors describing the periodic box, which need not be
> rectangular, of course.
> 
> Mark
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> 



-- 
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050916/043e2e4a/attachment.html>