[gmx-users] The number of lipids

[Kieu Thu Nguyen]

Sorry, i have one more question : Does genbox make new box that the area
per lipid is unchange (the same with the old box) ?

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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