[gmx-users] The number of lipids

[Justin Lemkul]

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)
>> --
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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

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