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 <[email protected]>wrote:
Thank Justin ! :-)
On Fri, Jan 11, 2013 at 5:26 PM, Justin Lemkul <[email protected]> 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 <[email protected]> wrote:
Kieu Thu Nguyen <[email protected]> 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 [email protected]
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 [email protected].
* 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 [email protected]
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 [email protected].
* 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 [email protected]
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 [email protected].
* 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
========================================
--
gmx-users mailing list [email protected]
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 [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
