Was your single molecule coordinate file energy minimised?
Did you look at the coordinate file for multiple molecules? In your grompp step before em, what is that coordinate file you are feeding to it? It has a different name to the one you generated using genconf. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9909 9304 --------------------------------- 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 C Johnson Sent: Thursday, 16 September 2010 10:06 AM To: [email protected] Subject: [gmx-users] Re Multiple Chains Sorry guys, I'm still learning the lingo. I want to simulate multiple molecules. This is what I tried: genconf -f polygly.pdb -nbox 2 2 2 -shuffle -o did_it_work.pdb Does this even seem like the right thing to do? I got to this part: grompp -v -f em -c b4em -o em -p speptide mdrun -v -s em -o em -c after_em -g emlog But I get an error that essentially tells me that my system needs to be energy minimized: Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 150 ] I'm guessing I'm pretty wrong in my approach to adding multiple molecules based on a single molecule pdb file. I'm determined to get this :)
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