On 2/4/13 4:53 AM, Ruben Cloete wrote:
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?
There is absolutely no need to reconstruct the entire system, otherwise what was
the purpose of the first EM? There are no fixed requirements for file formats;
Gromacs can handle just about anything. Use whatever you want.
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.
I have no idea why that would happen. The EM from steepest descents seems
perfectly reasonable. The seg fault could come from instability within the
system, but without a complete .mdp file there is no point in guessing.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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