From owner-chemistry@ccl.net Thu Sep  1 18:52:01 2011
From: "Tasaka Tomo t.tasaka(a)gmail.com" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: Freeware Amorphous Builder
Message-Id: <-45373-110901184900-27279-EKAO+3Nd3yugQbCOoFA3uw|,|server.ccl.net>
X-Original-From: Tasaka Tomo <t.tasaka(a)gmail.com>
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Date: Fri, 2 Sep 2011 07:48:52 +0900
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Sent to CCL by: Tasaka Tomo [t.tasaka . gmail.com]
Hello,

packmol is a useful tool to build an initial structure for such MD.
however, it seems to unsuitable for amorphous solids(e.g. no PBC
support).

if there are other recommended software packages which can build
amorphous solids/polymers, please advise. Or, do most people use a
cook and quench method with classical MD?

I appreciate any information you can provide.

Thanks,
Tomo

2011/8/26 Jussi Lehtola jussi.lehtola#,#helsinki.fi <owner-chemistry]=[ccl.net>:
>
> Sent to CCL by: Jussi Lehtola [jussi.lehtola*helsinki.fi]
> On Fri, 26 Aug 2011 02:49:50 -0400
> "Thomas Gkourmpis thomas.gkourmpis * borealisgroup.com"
> <owner-chemistry!=!ccl.net> wrote:
>> I am looking for a freely available amorphous builder for
>> constructing initial configurations of polymers using periodic
>> boundary conditions for molecular dynamics simulations. Can anyone
>> make any suggestions?
>
> Try packmol:
>
> http://www.ime.unicamp.br/~martinez/packmol/
> --
> --------------------------------------------------------
> Mr. Jussi Lehtola, M. Sc.         Doctoral Student
> jussi.lehtola!=!helsinki.fi         Department of Physics
> http://www.helsinki.fi/~jzlehtol  University of Helsinki
> Office phone: +358 9 191 50 632   Finland
> --------------------------------------------------------
> Jussi Lehtola, FM                 Tohtorikoulutettava
> jussi.lehtola!=!helsinki.fi         Fysiikan laitos
> http://www.helsinki.fi/~jzlehtol  Helsingin Yliopisto
> Työpuhelin: (0)9 191 50 632
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