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 <[email protected]> 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 <[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
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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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