[gmx-users] simulating two peptides in a box

kartik mehra hrahesh at gmail.com
Mon Jul 7 19:36:50 CEST 2008

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



PS: I have not yet tried the other suggestion of translation and rotation
followed by concatenating the two files
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