[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
>>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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