[gmx-users] some prolem about genbox genconf and editconf

DreamCatcher huangshuping1987 at gmail.com
Wed Oct 28 03:50:11 CET 2009

Hi everybody,
     I have come across some problem when using genbox, genconf and editconf
try to make a box with a certain density and a certain number of polymer
First, I use genbox to have one polymer chain filled in the box without any
solvent.Then I use genconf to pile up 27 polymer chains ,after that I use
editconf to designate a density of  0.3 g/ml to attain the final goal. When
I finish it, i find that all the bond that connect the atoms are gone and
all the atoms disperse in the box.
    In another try, I first use a pdb file which contains only one polymer
chain to genconf a box with 27polymer chain, and then use editconf to
designate the density, but finally I get a box with lots of bonds that might
not present in a normal structure, like a carbon was bonded with a 3 or 4 or
even more atoms distance long and the bonds connect with it is overcount.
What is the prolem? How can I fix it?

Thanks in advance,
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