Hi Justin i see lots of papers perform steepest descent followed by
conjugated gradients.
My question do i use the .gro output file as input to perform conjugated
gradient minimization as shown in the commands below? or do i repeat
pdb2gmx, editconf and genbox on the trajectory file (protA_em.trr) which
i must convert to a .pdb file?
nohup mdrun -s protA_em.tpr -o protA_em.trr -c *protA_b4pr.gro* -g
em.log -e em.edr &
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 1000
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 1000 in 754 steps
Potential Energy = -6.8864319e+05
Maximum force = 9.1053461e+02 on atom 499
Norm of force = 2.2879843e+01
Now i run conjugated gradient (500 steps)
grompp -f em2.mdp -c *protA_b4pr.gro* -p Rv1712.top -o protA_1em.tpr
nohup mdrun -s protA_1em.tpr -o protA_em1.trr -c protA_b4pr_1.gro -g
em.log -e em.edr &
when i run these i get an error message segmentation fault? which i know
is usually a memory problem.
Thanks
Ruben
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