[gmx-users] Re: [gmx-developers] Hexagonal prism

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 19 13:30:02 CET 2004

On Wed, 18 Feb 2004, Simon Wang wrote:

>Hi, GMX users:
>I got a little bit confused about how to define a hexagonal unit cell as a 
>special case of triclinic cell. When using "editconf -f conf.gro -o out.gro 
>-bt tric -box 5 5 3 -angles 90 90 120 -c" to assign the values of a, b, c, 
><bc, <ac, <ab, followed by conversion of "trjconv -pbc inbox -ur compact" or 
>"trjconv -pbc whole -ur compact", I can get the right shape of hexagonal 
>prism. But the SIZE of the hexagonal edge is about 30 angstrom, not 50 as 
>defined. I guess I don't fully understand the way GROMACS define the 
>triclinic cell. I hope someone can help me out.

manual chpater 3
 (with figures)
>>From: David van der Spoel <spoel at xray.bmc.uu.se>
>>Reply-To: gmx-users at gromacs.org
>>To: Simon Wang <sim_wang03 at hotmail.com>
>>CC: gmx-users at gromacs.org
>>Subject: [gmx-users] Re: [gmx-developers] Hexagonal prism
>>Date: Wed, 18 Feb 2004 11:25:59 +0100 (CET)
>>On Tue, 17 Feb 2004, Simon Wang wrote:
>> >Hi, David:
>> >
>> >I've installed GROMACS 3.2.0 and tried the new version of trjconv.
>> >Unfortunately I still could not get the right size of hexagonal prism. I
>> >tried the following things:
>> >trjconv -pbc whole -ur compact
>> >trjconv -pbc com -ur compact
>> >
>> >However, there is no option like "compact" for -pbc. If this is a bug, do
>> >you ever have plan to fix it in the near future?
>>it's not necessary.
>>trjconv -pbc inbox -ur compact does what you want.
>>please put further questions to the mailing list only.
>> >
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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