[gmx-users] editconf

[David van der Spoel]

On Tue, 16 Apr 2002, Nguyen Hoang Phuong wrote:

>
>the box size of the my simulation box is 4nm and d is 1.0. In the ouput
>file there are some atoms of the solute whole coordinates have negative
>values. GROMACS sets the origin of the coordinate frame at the corner of
>the box, isn't it?

It is molecule size + 2d (distance to the edge of the box).

Origin is at one corner.


>Phuong
>------
>On Tue, 16 Apr 2002, David van der Spoel wrote:
>
>> On Tue, 16 Apr 2002, Nguyen Hoang Phuong wrote:
>> 
>> >
>> >Hi All,
>> >
>> >there is an option -d in the program editconf. Is it the distant between
>> >the center of mass of the solute and the box or the minimum solote-to-wall
>> >distance?
>> The latter, otherwise it would be just half the box size
>> -- 
>> 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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>

-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++