[gmx-users] Question regarding the minimization of the system

[ali.khourshaei71 at student.sharif.edu]

Dear Justin, 

Thanks for your kindly response. But, I'm still a little confused. In
the mentioned draft, it is pointed out that: 

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In order to energy minimize our system a .tpr file is generated using
grompp by using an .mdp file and a topology
corresponding to pure DPPC. The energy minimization script is: 

;title = Minimization of DPPC Bilayer
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 100.0 ; Stop minimization when the maximum force < 100.0
kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 10000 ; Maximum number of (minimization) steps to perform
tinit = 0.0
dt = 0.025
nstlist = 1 ; Frequency to update the neighbor list and long range
forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME
rcoulomb = 1.2
vdw_type = cut-off
rvdw = 1.2
pbc = xyz ; Periodic Boundary Conditions
tcoupl = no
pcoupl = no
gen_vel = yes
gen_temp = 310
gen_seed = 173529
epsilon_r = 15
constraints = none
nstxout = 100
nstvout = 100
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 100
xtc_precision = 1000 

Before running grompp, use editconf to convert .pdb file to .gro file
and then run grompp on the generated .gro file.
grompp -f minim.mdp -c dppc128.gro -p topol.top -o em.tpr
The .tpr file contains information about bonding and periodicity so it
can, in a sense, be used to reconstruct
"broken" molecules.
Run trjconv to remove periodicity:
trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur
compact
Run grompp again with the compact structure:
grompp -f minim.mdp -c dppc128_whole.gro -p topol.top -o em.tpr
Invoke mdrun:
mdrun -v -c dppc_minimised.gro 

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So, since it used pbc= xyz in the .mdp file, I think using trjconv for
removing periodicity is meaningless. Isn't it? If not, since until now I
minimized the system without removing its periodicity, was my previous
molecular dynamic simulations false? 

Thanks in advance, 

Ali