[gmx-users] parameter on Energy Minimization

Liu Shiyong liushiyong at gmail.com
Tue Mar 11 19:24:12 CET 2008


I used a script given below for energy minimization of  a native
protein-protein complex 1akj.

I removed HETATMs and water molecules from the structure, and the minimized
structure  (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80.
Then I used rasmol to check the result.  The ligand is ran away from
 rasmol 1akj_oplsaa.minim_traj.pdb

Then I tried the larger epsilon_r           =  800000.0, and got very
similar result. I mean that for two substantially different values of the
epsilon_r minimization gives absolutely the same final positions of the

I also tried difference forcefield encads, encadv, G43a1, G43a2, G43b1,
G45a3, G53a5, G53a6,  gmx, oplsaa.
I also got similar result.


pdb2gmx   -ff oplsaa -f 1akj_oplsaa.pdb -p 1akj_oplsaa.top -o
1akj_oplsaa.gro -i 1akj_oplsaa.itp > 1akj_oplsaa.
output.pdb2gmx 2>&1 &

grompp -f em.mdp -c 1akj_oplsaa.gro -p 1akj_oplsaa.top -o
1akj_oplsaa.input.tpr > 1akj_oplsaa.output.grompp
2>&1 &

mdrun -nice 0 -v -s 1akj_oplsaa.input.tpr -o 1akj_oplsaa.minim_traj.trr -c
1akj_oplsaa.minimized.gro -e

minim_ener.edr > 1akj_oplsaa.output.mdrun 2>&1 &

 trjconv  -f 1akj_oplsaa.minim_traj.trr -s 1akj_oplsaa.input.tpr -o
1akj_oplsaa.minim_traj.pdb << HHH

em.mdp is :

title               =  1akj_oplsaa
cpp                 =  /usr/bin/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
dt                  =  0.002    ; ps !
nsteps              =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         =  cut-off
epsilon_r           =  80.0
rcoulomb            =  1.8
vdwtype             =  cut-off
rvdw                =  1.8
;       Energy minimizing stuff
emtol               =  10.0
emstep              =  0.01

Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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