[gmx-users] The number of lipids

Sun Jan 13 17:12:13 CET 2013

Thank Justin !
It is so hard to get the right APL in the new box (after genbox step) ! How
can i predict the new box size (that made after energy minimization) ? The
box is compressed after running EM.

On Sat, Jan 12, 2013 at 6:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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)
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>>>>>>  --
>>>> ==============================****==========
>>>>
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Research Scientist
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
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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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