[gmx-users] The number of lipids

[Justin Lemkul]

On 1/12/13 6:17 AM, Kieu Thu Nguyen wrote:
> Sorry, i have one more question : Does genbox make new box that the area
> per lipid is unchange (the same with the old box) ?
>

genbox reads in the old coordinates and uses them to build a grid within the new 
box.  It will not write partial molecules, so in the case of lipids, you may be 
left with rather large voids in the new box.  Thus you would need fairly 
extensive equilibration to prepare the system and hopefully achieve the proper APL.

So no, genbox does not guarantee this for you.

-Justin

> On Fri, Jan 11, 2013 at 7:04 PM, Kieu Thu Nguyen <kieuthu2212 at gmail.com>wrote:
>
>> Thank Justin ! :-)
>>
>>
>> On Fri, Jan 11, 2013 at 5:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 1/10/13 11:37 PM, Kieu Thu Nguyen wrote:
>>>
>>>> Thank Justin and Peter so much !
>>>> Can i make a new box (it's size is not a multiples of the size of the
>>>> previous box) from a smaller lipid bilayer box ?
>>>>
>>>> I don't see genconf -nbox can do that.
>>>>
>>>>
>>>>
>>> genbox -cs old_lipids.gro -box x y z -o new_lipids.gro
>>>
>>> Just make sure you get a sensible number of lipids per leaflet.
>>>
>>> -Justin
>>>
>>>
>>>
>>>> On Fri, Jan 11, 2013 at 9:20 AM, Peter Lai <pcl at uab.edu> wrote:
>>>>
>>>> Kieu Thu Nguyen <kieuthu2212 at gmail.com> wrote:
>>>>>
>>>>> Dear All,
>>>>>>
>>>>>> I see in MD simulations, the number of lipids is 128 or multiples of
>>>>>> 128.
>>>>>> Can someone tell me why ?
>>>>>> Whether can i choose another number of lipids ?
>>>>>>
>>>>>> Thanks in advance !
>>>>>> KT
>>>>>> --
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>>>>>>
>>>>>
>>>>> probably because they are using original 128-lipid coordinates from
>>>>> someone like tieleman or klauda. You can use any arbitrary # of lipids
>>>>> appropriate to the size of your intended system (like scaling it so
>>>>> that an
>>>>> embedded protein is shielded by lipids from its periodic image)
>>>>> --
>>>>> Sent from my Android phone with K-9 Mail. Please excuse my brevity.
>>>>> --
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>>>>>
>>> --
>>> ==============================**==========
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>
>>> ==============================**==========
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>>
>>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================