[gmx-users] steepest descents followed by conjugated gradient

Ruben Cloete ruben at sanbi.ac.za
Mon Feb 4 10:53:33 CET 2013

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.


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