[gmx-users] genbox

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 14 23:47:00 CEST 2011

leila separdar wrote:
> I have .gro and .top of a nanoparticle at temperature 1K and I want to
> add the simulation box some other atomes at temperature 300K. is there
> any body knows how can I do it. I have  used (genbox -cp
> nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it
> add more than atomes than I expect for example if there is 600 other
> atomes in otheratom,gro file this command add 2000 atomes to
> simulation box and also nanoparticle.top does not update.
> thanks in advance

The -ci option should be used in conjunction with -nmol, and the configuration 
contained in -ci (I believe) cannot contain multiple molecules.  If you want 600 
molecules/atom to be inserted, provide a configuration of a single molecule/atom 
and specify -nmol 600.

With respect to the topology not being updated, that is to be expected.  The -p 
option only works for water (unfortunately).



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


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