Re: [gmx-users] Re: gmx-users Digest, Vol 53, Issue 81

[Justin A. Lemkul]

sudheer babu wrote:



 
Thanks to Jochen


   To increase the lipid molecule number from 128(which downloaded from 
Dr.Tieleman site) to more than 158, I issued this command
   genbox -cs 128popc.gro -o out.gro -box 9.2 9.2 6.3 but in the output 
file it showed unequal  amount water molecules on both leaflets, I have 
tried in changing the box values in many ways but I couldnt able to get.
   Can any tell me how can I solve this problem to get increase in popc 
molecules with equal amount of water on both leaflets.


There are a couple options.

1. Start with a bigger lipid "solvent," created with genconf (i.e., genconf 
-nbox 2 2 1 will give a system that starts with 512 lipids)


2. Use a z dimension that corresponds to the original POPC bilayer.  There are 
two POPC structures available at Tieleman's site, neither of which have a 
vertical box dimension of 6.3.  So, unless you have made some modifications to 
the dimensions of the box, you should start by trying the original z box size, 
if it will adequately accommodate your system.  If your box size is incorrect, 
genbox tries to overlay more of the "solvent" box into your system, which is 
probably why you're getting an uneven distribution of water.


3. Make sure your system is centered within the box.

-Justin


Thanks in advance.




I guess that depends on the size of your protein. You should have enough
 lipds such that the protein doesn't interact with its preriodic image.
90 POPC seem to be a bit to few for that. In my aquaporin simulations, I
usually had something like 270 POPE molecules, but if you simulate a
smaller protein, less lipids may be sufficient. You may also want to use
a hexagonal box which will allow you have less lipids and water.

cheers, jochen

sudheer babu wrote:
 > Hi gmx-users,
 > whats the number of POPC molecules should be there after
inserting protein
 > into popc? In my case 90 popc molecules are there around the
protein from
 > 128 molecues which I downloaded from Dr.Tielman's website.
 >
 > Any suggestion will be appreciated
 > Thanks in advance.
 >
 >
 >
 >

 >
 >
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de 
Tel.: +49 (0)551 201-2312



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Justin A. Lemkul
Graduate Research Assistant
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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[gmx-users] Re: gmx-users Digest, Vol 53, Issue 81

[sudheer babu]

 

>
> Thanks to Jochen
>
   To increase the lipid molecule number from 128(which downloaded from
Dr.Tieleman site) to more than 158, I issued this command
   genbox -cs 128popc.gro -o out.gro -box 9.2 9.2 6.3 but in the output file
it showed unequal  amount water molecules on both leaflets, I have tried in
changing the box values in many ways but I couldnt able to get.
   Can any tell me how can I solve this problem to get increase in popc
molecules with equal amount of water on both leaflets.
Thanks in advance.

>
>
>
> I guess that depends on the size of your protein. You should have enough
>  lipds such that the protein doesn't interact with its preriodic image.
> 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I
> usually had something like 270 POPE molecules, but if you simulate a
> smaller protein, less lipids may be sufficient. You may also want to use
> a hexagonal box which will allow you have less lipids and water.
>
> cheers, jochen
>
> sudheer babu wrote:
> > Hi gmx-users,
> > whats the number of POPC molecules should be there after inserting
> protein
> > into popc? In my case 90 popc molecules are there around the protein from
> > 128 molecues which I downloaded from Dr.Tielman's website.
> >
> > Any suggestion will be appreciated
> > Thanks in advance.
> >
> >
> >
> > 
> >
> >
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
> 
>
>
> --
>
> ___
> gmx-users mailing list
> gmx-users@gromacs.org
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>
> End of gmx-users Digest, Vol 53, Issue 81
> *
>
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