[gmx-users] steepest descents followed by conjugated gradient

Justin Lemkul jalemkul at vt.edu
Mon Feb 4 14:38:28 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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