From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Mon Sep 09 2013 - 15:50:18 CDT
Well, I've done that, downloaded and installed topotools1.3.
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
To: Richard Wood <rwoodphd_at_yahoo.com>
Cc: NAMD list <namd-l_at_ks.uiuc.edu>
Sent: Monday, September 9, 2013 3:15 PM
Subject: Re: namd-l: bilayer creation
On Mon, Sep 9, 2013 at 9:58 PM, Richard Wood <rwoodphd_at_yahoo.com> wrote:
> I have built a small system in VMD. Where do i find this replicatemol
it is shipped with VMD.
but since the last release of VMD has been quite a long time ago, you
may be better off to download the latest test version of VMD (which
contains updates with new features and bugfixes) or at least download
and install the latest plugin version from my homepage.
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: Richard Wood <rwoodphd_at_yahoo.com>
> Cc: NAMD list <namd-l_at_ks.uiuc.edu>
> Sent: Monday, September 9, 2013 2:15 PM
> Subject: Re: namd-l: bilayer creation
> On Mon, Sep 9, 2013 at 9:00 PM, Richard Wood <rwoodphd_at_yahoo.com> wrote:
>> Hi all,
>> I apologize in advance if I am asking this in the wrong place, but I've
>> looked elsewhere.
>> I'm trying to build a bilayer of phospholipids and I need to know what is
>> the biggest bilayer that I can build. I've found that I can build about a
>> 50 by 50 lipid leaf in VMD; I'm wondering if there is somewhere that I can
>> build something larger than that. I'd also prefer to use a lipid like
>> and not POPC.
>> I'd appreciate either answers to these questions or a pointer to where I
>> find answers.
> build a small system with whatever tool you like or pick a properly
> pre-equilibrated system, make sure you have the proper system
> dimensions and replicate it as many times as you like. in VMD this can
> for example be done with the Topotools::replicatemol command.
>> Richard Wood
>> Purdue University Calumet
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
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