[gmx-users] (no subject)

[Erik Lindahl]

mojtaba alaei wrote:
> 
> Dear All
> 
> In http://www.gromacs.org/benchmarks/index.php,There is a file with this
> name:gmxbench-3.0.tar.gz,and in this file there is a folder,d.poly-ch2,
> who did generate this folder?and how can he generate topol.top and 
> conf.gro?

Hi,

That topology was generated manually by a former PhD student in the 
polymer group in Stockholm; unfortunately he's left the academic world
by now, so it's not of much help...

The configuration was generated by starting from an extended 
conformation in a VERY large box, and then letting it condense while 
simulating at 600K with 1 fs timesteps (no bond constraining because
of the very large molecule).

I believe he got most parameters and procedures from the work of Boyd
and coworkers, but I'm not a homopolymer expert :-)

Cheers,

Erik