supti mukherjee wrote:
Dear all,
I was minimising a protein structure. I added polar hydrogens to the
protein by some program and then proceeded for the energy minimisation.
I chose Conjugate Gradient of 1000 steps with emtol as 100. The mdrun
came out with the following error.
" 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 ..
17052 ]"
Can anybody please help me in identifying my mistake?
Try the general procedure outlined here...
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
