Dear GMX Users, I am trying to set up a simulation box with two proteins. I have perused the archives about the methodology of doing so. I tried the recommended option of changing the number of protein molecules in the topology file to 2. However when I run grompp after editconf and genbox, I get warning that the number of co -ordinates do not match (since I had not updated the number of solvent molecules ...) After updating the number of solvent molecules, when I try running grompp again, it shows a warning that the 23644 atom names do not match in top and gro files and that atom names from top files are being chosen .
Upon subsequent mdrun, the system explodes after a 1-4 interaction warning. I was wondering whether anyone could help me out on this ... I do understand that the topic has been discussed pretty often but would appreciate any help ... Cheers Kartik PS: I have not yet tried the other suggestion of translation and rotation followed by concatenating the two files
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