[gmx-users] Re: How to generate the initial coordinates file?

Justin A. Lemkul jalemkul at vt.edu
Tue May 29 22:21:14 CEST 2012

On 5/29/12 4:19 PM, Bao Kai wrote:
> Hi, Justin,
> Thank you very much for your help.
> It seems that genbox will need really huge memory even with thousands
> of molecules.
> If we want to to further to tens or hundreds of thousands molecules,
> do we need some cluster to run genbox in parallel?

genbox is not parallelized.  If you need to create a very large system, create a 
smaller system and replicate it with genconf -nbox.  If memory is still an 
issue, consider whether or not you need such a large system ;)



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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