From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Mon Sep 09 2013 - 14:58:39 CDT
I have built a small system in VMD. Where do i find this replicatemol command?
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 DMPC
> and not POPC.
> I'd appreciate either answers to these questions or a pointer to where I can
> 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.
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