AMBER Archive (2009)

Subject: Re:Re: [AMBER] box problem

From: Nancy (
Date: Mon Aug 17 2009 - 21:49:20 CDT

Thank you case.I use command set unit box {x y z} to add a periodic box to my unit ,the box size is equal to unit size. But i don't known how xleap execute this command,can it find where my unit located? if not ,where the box center on ? So can you give me a explain? Thanks in advance.

2009-08-13case <> д
>On Thu, Aug 13, 2009, Nancy wrote:
>> I use command set unit box {x y z} in xleap to add a rectangular box
>> to my unit,but there is interspace between box and unit ,ir there any
>> method that i can add a periodic box to my unit without interspace with
>> the unit.
>Can you explain more fully what you mean by "interspace between box and unit"?
>If you set the box as above, LEaP uses those values, independent of where any
>atoms might be located. Are you sure that you have chosen the best values for
>x,y and z? Are you sure you want to use that command? What are you trying to
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