On 10/3/12 1:59 AM, James Starlight wrote:
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) ?
genbox decides whether or not to put molecules in the box if they can be added
intact; anything sticking out of the box is removed. Since water molecules are
small, this is easy to do. Since a lipid molecule is large, it is not so easy.
The hydrocarbon tails are very flexible and thus may have configurations
leading them to stick out of the box, so genbox won't add them. You will likely
have to gradually increase the box dimensions in x and y to allow for more
lipids to be added, striking a balance between the (much larger) number of water
molecules and number of lipids added.
-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@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
