[gmx-users] Coordinate file for lipid bilayer

[James Starlight]

Justin,

I've told about lower lipid density at the left and right edges of the
new system ( see new pic bellow with marked regions).

http://imageshack.us/photo/my-images/10/dppc.png/

I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10

I've created new box with the desired sizes for my system as well as
centered it in it. Finally I've resized it via
genbox -cp prot_in_lipids_old.gro -cs dppc128_whole.gro -box 8.04542
8.04542  10.19156


As the result I've obtain syste of 128 lipids and 13000 water with dims 8x8x10

I have the same system with the popc lipids with the same dims where
there are 200 lipids

Why only 10 lipids were added after resizing ? How I could increase
this number of added lipids ( expesially in regions with lower lipid
density- see pic) ?


James

2012/10/2, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 10/2/12 4:12 PM, James Starlight wrote:
>> This is exactly what I've obtained
>>
>> http://imageshack.us/photo/my-images/27/89293914.png/
>>
>
> This looks completely normal.  What I was asking for was an image of one of
> your
> failed attempts that has whatever odd manifestation you've been trying to
> describe.
>
>> the same effect was also in case of intact tieleman's lipid bilayers (
>> the water layers were broader than lipid after resizing with genbox)
>>
>
> Sorry, I still don't understand.  I've explained as clearly as I can how to
>
> proceed, if you need further help you will have to provide the exact
> commands
> you're using and why they're insufficient (again, pictures of failed
> systems,
> not normal ones, would help here).
>
> -Justin
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> 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
>