[gmx-users] The number of lipids

[Justin Lemkul]

On 1/13/13 11:12 AM, Kieu Thu Nguyen wrote:
> 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.
>

Generally you need rather extensive equilibration (tens or hundreds of ns) to 
achieve a correct APL, which is also a function of the quality of the force 
field parameters.  Simply generating a configuration or running it through EM is 
not enough.

-Justin

>
> 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
>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
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>>>>>>
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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

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