[gmx-users] Membrane simulations

[Björn Sommer]

Hi Stephan,

I also think you mean PackMol, because we are not from Brazil ;-)

However, you can also directly write if you have questions concerning 
the MembraneEditor. Usually the idea is that you just use our WebStart 
application and feel happy with it:

http://cellmicrocosmos.org/index.php/start/startcm2

So you usually will not require to dig into the source code. For packing 
algorithms development, we have developed a special interface which is 
discussed here:

http://cellmicrocosmos.org/index.php/developer/introduction

Second, I made 2013 a small review concerning Membrane Packing Problems, 
there are several tools listed:

http://journals.sfu.ca/rncsb/index.php/csbj/article/view/csbj.201302014/247

Happy membrane modeling in any case!
Björn

P.S.: If you want to analyze the Area per Lipid or Thickness of your 
lipid membrane after your simulation, you should have a look at 
APL at Voro, it is really a nice program!


Am 14.08.2014 12:00, schrieb 
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>     1. Re: Membrane simulations (Victor Rosas Garcia)
>     2. Re: Membrane simulations (lloyd riggs)
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> Message: 1
> Date: Wed, 13 Aug 2014 16:09:14 -0500
> From: Victor Rosas Garcia <rosas.victor at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Membrane simulations
> Message-ID:
> 	<CAJota7DMxabmtro5nRwN3wiCTCQNC3YSmk_bHEeW1+j_Y6Q7eg at mail.gmail.com>
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> Hello Stephan,
>
> Do you mean PACKMOL?
>
> http://www.ime.unicamp.br/~martinez/packmol/
>
> VIctor
>
> 2014-08-13 0:58 GMT-05:00 lloyd riggs <lloyd.riggs at gmx.ch>:
>> Dear GMX users,
>>
>> I ran across a nice web page, I believe from a brazilian group, for
>> generating membranes of any compnents (pdb).  This was months ago, and after
>> a few days of trying, I cannot find the page again.  It was capable of
>> makeing bilayers, as well as other shapes, including small micelle's.  I
>> have already looked at
>> http://www.cellmicrocosmos.org/index.php/download/downloadcm2 , and all
>> relavant gromacs tutorials, as well as links to find them...so any help is
>> appricaited.  They have nice readable source code, and the scripts were
>> simple and freeware.
>>
>> Sincerly,
>>
>> Stephan Watkins, PhD
>> OSU botany department
>>
>>
>>
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> Message: 2
> Date: Thu, 14 Aug 2014 05:08:53 +0200
> From: "lloyd riggs" <lloyd.riggs at gmx.ch>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Membrane simulations
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