[gmx-users] How to make a lipid bilayer with specific dimensions?
NG HUI WEN
HuiWen.Ng at nottingham.edu.my
Tue Sep 28 04:13:23 CEST 2010
Points noted, thanks Justin!
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Tuesday, September 28, 2010 10:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to make a lipid bilayer with specific
dimensions?
NG HUI WEN wrote:
> Thanks for that guys! I will try them out.
>
> Just a quick question here with regards to my lipids being possibly
too
> small, does it have something to do with the minimum image criterion
> for PBC? I have ensured that the distance of edge of the box and the
> atoms at the side of the protein to be greater than the cutoff of
1.2nm
> (PME is used)... in the hope that the protein would not interact with
> it's neighbouring image. I hope I'm not going down the wrong direction
> in my understanding of pbc...
>
> Thanks!!!
>
There is no direct relationship between genbox and the minimum image
convention.
You certainly need to build a system that is of sufficient size to
avoid
spurious PBC interactions, but when genbox does is independent of this
fact.
The problem is that genbox will not place a molecule that falls
partially
outside the box, thus deleting an entire lipid and leaving a gap at the
edge of
the box. Like Chris said, this can lead to your system compressing
somewhat to
give dimensions smaller than what you were hoping for. Whether or not
this is a
problem in the long run is up to you to decide based on the specifics of
your
system.
Short answer: make your box slightly larger than you think you need and
equilibrate for a long time to ensure that your box is stable.
-Justin
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of
> chris.neale at utoronto.ca
> Sent: Monday, September 27, 2010 8:30 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] How to make a lipid bilayer with specific
> dimensions?
>
> I don't think that this is currently causing anybody any problems, but
> note that genbox is going to cut any lipids that cross out of the
> central unit box (either because genbox is unaware of PBC or because
> these lipids now clash across PBC).
>
> Therefore:
>
> genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
>
> will give you a bilayer that gets solvated with a water defect around
> the edges of the initial unit cell and that, after 10 - 200 ns of
> simulation, gives you an equilibrated bilayer (without water defect)
> that is much smaller than x=9.6, y=9.5.
>
> To get what you want, you need to either start your bilayer with
> larger x and y (calculate area per lipid in 9.6*9.5 to figure out how
> many lipids you should have and keep running genbox until you get
> that), or perhaps a run through inflategro might do it.
>
> Chris.
> --original message --
>
> [gmx-users] How to make a lipid bilayer with specific dimensions?
> Justin A. Lemkul jalemkul at vt.edu
> Mon Sep 27 13:00:32 CEST 2010
>
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>
> NG HUI WEN wrote:
>> Dear gmxusers,
>>
>> I am trying to make a lipid bilayer with specific dimensions using
>> gromacs. So far, I have got up to:
>>
>> 1) Download a lipid POPC128a.pdb from Peter Tieleman?s website
>>
>> 2) Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2 2 1 to
>> multiply the lipid in the x and y axis. The resultant output was a
>> lipid with box vectors 12.478 , 12.359 and 6.919 (nm)
>>
>> My ultimate aim is to generate a POPC bilayer with the dimensions
>> 9.600 9.500 and 14.000. Currently, the lipid bilayer is too big. I
>
> Too big? If you're using either of the two coordinate files above
> (popc128a.pdb, popcx2.pdb), they should be too small.
>
>> would like to ?crop? the excess lipids to the required size if at
>> all possible. I tried using editconf ( a bit of a long shot) to make
>> a new box size. The new structure file has a CRYST1 of 9.600 9.500
>> and 14.000 but when I view it with VMD, it is not any smaller than
>> before.
>>
>> Do I have to use other software to achieve this? If so, I?d really
>> appreciate some pointers.
>>
>
> You can do this in three steps. If your goal is to have a single
> lipid bilayer
> in the middle of the box, with water around it:
>
> genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
> editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14
> genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb
>
> The reason you need three steps is that if you supply a z-dimension of
> 14 in the
> first genbox command, at least two full bilayers (or some fraction
> close to it)
> will be placed in your box. If that's your goal, then this can be
> done in one step.
>
> -Justin
>> Thanks!
>>
>> <<
>>
>> Email has been scanned for viruses by UNMC email management service
>> <http://www.nottingham.edu.my>
>>
>> >>
>>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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