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 [email protected] +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of DreamCatcher Sent: Wednesday, 28 October 2009 1:50 PM To: [email protected] 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, Celeste
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