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

[Justin A. Lemkul]

sudheer babu wrote:
> <http://www.gromacs.org/mailman/listinfo/gmx-users>
> 
>      
>     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 <http://gwdg.de>
>     Tel.: +49 (0)551 201-2312
>     ************************************************
> 
> 
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>     End of gmx-users Digest, Vol 53, Issue 81
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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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