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Bessel

木虫 (正式写手)

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jiaoyixiong: 金币+3, 鼓励交流 2012-12-18 15:31:26
dyc_2008: 金币+3, ★★★★★最佳答案, 太详细了这个 2012-12-18 15:44:41
zh1987hs: 金币+1, 模拟EPI+1, 回答清楚~应要求授予EPI一枚~鼓励多多发言! 2012-12-27 08:16:34
If you know how to construct a LAMMPS data file for a single molecule,
then you can use the "moltemplate" program to build complex periodic
structures with it.

http://www.moltemplate.org

In addition to "moltemplate" there are several other modeling programs:

http://sites.google.com/site/akohlmey/software/topotools
http://sourceforge.net/projects/moleculardynami/

Here are some pictures of simulations we have run in LAMMPS built with
moltemplate:

http://lammps.sandia.gov/images/ ... ayer32x37_t=0ps.jpg
http://lammps.sandia.gov/images/ ... _rainbow_t=80ps.jpg
http://www.moltemplate.org/image ... ane+watMW_t=0ps.jpg
http://www.moltemplate.org/image ... tein_t=0ps_side.jpg
http://www.moltemplate.org/image ... otein_t=0ps_top.jpg

If you want to use "moltemplate" you must first build a file which
describes the molecule (or molecules) you want to use to build your
liquid crystal.  (This file can be in either lammps "DATA" format, or
"LT" format.)  Moltemplate can not do this automatically, but you can
build the molecule by hand if it is not complicated.  This is what I
usually do for my simple molecules.  Otherwise you can use
VMD/topotools or "Molecular Dynamics Studio" to create a DATA file for
a single molecule (see links above).  Then you can import it into
moltemplate.

Currently, you must manually specify ALL of the parameters for the
force-field you want to use.  (There is no way to infer the
force-field parameters automatically from atom-type.)  This is the
difficult part of setting up the simulation.  However you have
complete freedom to use any force-field you want.
7楼2012-12-18 15:29:15
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