[gmx-users] The number of lipids

[Kieu Thu Nguyen]

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
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>
>>>
>>> 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.
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> * Please search the archive at
>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>
>>>
> --
> ==============================**==========
>
> 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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>