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

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Wed Oct 28 04:23:23 CET 2009

How are you visualizing the system?  Using VMD?  In that case, bonds are
determined by how far apart the atoms are, it guesses what the bonding
is, since a .gro file (or a pdb) doesn't have any bonding information in
it.  So what you are seeing is simply the fact you have scaled the box,
increasing or decreasing the distance between the atoms.  After a quick
EM the atoms will return to their correct spacing.


Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology 
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of DreamCatcher
Sent: Wednesday, 28 October 2009 1:50 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] some prolem about genbox genconf and editconf


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 chains.

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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