[gmx-users] Reg: Adding multiple molecules

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 27 13:01:10 CEST 2010

vinothkumar mohanakrishnan wrote:
> Hi all
> I have a diffculty in adding multiple molecules of hexane to my box. my 
> box size is 4.72*2.36*2.36 (nm) according to my number density 
> calculations the box should fit 124 molecules of hexane whereas it adds 
> only 76 molecules to the box below is my command. i had evev tried with 
> -try command but without sucess.
> genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o 
> hexane-multi.gro -nmol 124 -seed 1268

If you're not getting all the molecules you want, then genbox is unable to find 
sufficient space for them.  Try a larger box, then equilibrate.


> Regards
> Vinoth


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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