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

[Mark Abraham]

Hi,

The notion of "removing periodicity" is not the most appropriate one. There
are infinitely many equivalent representations. Trjconv permits you to
choose a different one than was chosen when the file was written. Mdrun
will of course be happy with whatever it wrote out last time.

Mark

On Sun, 19 Feb 2017 16:21 <ali.khourshaei71 at student.sharif.edu> wrote:

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