[gmx-users] NPT for compressing the system

Moeed lecielll at googlemail.com
Wed Jul 14 05:09:31 CEST 2010


Thank you for suggestions. Yes simulation crashes. I am not able see the
whole run (1000ps). For all pressures I tired the final simulation box is
2.2*2.2*2.2 nm but simulation crashes before 1000ps. The longest simulation
is for 120 bar (727ps). and I think that is why I am not getting the
_after_md.gro file after mdrun in none of the simulations. I wanted to take
that convoluted structure and replicate the box..

mdrun -s PE60-P120_md.tpr -o PE60-P120_md.tpr -c PE60-P120_after_md -v
>& output.mdrun_md

As you suggested I do the runs in stepwise manner. I need still a little
smaller box size than 2*2*2 but I noticed sth during these simulations. When
I view the trajectory in ngmx on the menu bar I can select type of box. When
I select triclinic or octahedron the final confromation of the chain is more
convoluted and fits completely in the box while in case of rectangular box
except for pressure of 120 bar for all other pressures I tried most parts of
the chain remain outside of the small box. molecules is more extended...I am
wondeirng if positions of atoms are calculated and stored how changing the
box type in trajectory viewer can affect the structure?!
file I used:
title               =  PE-Hexane

;define           =  -DPOSRES    ; tells gromacs to perform position
restrained dynamics/include posre.itp into topology used for position
pbc              =  xyz        ; use priodic BCs in all directions

;        Run control
integrator          =  md        ; type of dynamics algorithm. Here md uses
a leap-frog algorithm for integrating Newtons's eq of motion
dt                  =  0.002        ; in ps !
nsteps              =  500000        ; length of simulation=
nstcomm             =  1        ; frequency for center of mass motion

;        Output control
nstenergy           =  100        ; frequency to write energies to energy
file. i.e., energies and other statistical data are stored every 10 steps
nstxout             =  100        ; frequency to write
coordinates/velocity/force to output trajectory file. how often snapshots
are collected= nstxout*dt
nstvout             =  100
nstfout             =  0
nstlog              =  100        ; frequency to write energies to log file
nstxtcout          =  10        ; frequency to write coordinates to xtc

;        Neighbor searching
nstlist             =  10        ; frequency to update neighbor list.
Neighborlist will be updated at least every 10 steps. Manual p80
ns_type             =  grid        ; make a grid in the box and only check
atoms in neighboring grid cells when constructing a new neighbor list every
nstlist steps

;        Electrostatics/VdW
coulombtype         =  Shift        ; tells gromacs how to model
electrostatics. Coulomb/LJ potential is decreased over the whole range and
forces decay smoothly to zero between
vdw-type            =  Shift      ; rcoulomb-switch/rvw-switch &
rcoulomb-switch     =  0        ; where to start switching the Coulomb
rvdw-switch         =  0        ; where to start switching the LJ

;        Cut-offs
rlist               =  1.1        ; in nm. Cut-off distance for short-range
neighbor list
rcoulomb            =  1.0        ; distance for coulomb cut-off
rvdw                =  1.0        ; distance for coulomb cut-off

;        Temperature coupling
Tcoupl              =  berendsen
tc-grps             =  System  ;HEX            ; groups to couple to
thermostat; Berendsen temperature coupling is on in these groups
tau_t               =  0.1     ;0.1            ; time constant for T
ref_t               =  300     ;300            ; reference T for coupling.
When you alter the T, don't forget to change the gen_temp for velocity

;        Pressure coupling
Pcoupl              =  berendsen    ; Pressure coupling is not on
Pcoupltype          =  isotropic     ; means the box expands and contracts
in all directions (x,y,z) in order to maintain the proper pressure
tau_p               =  0.5        ; time constant for coupling in ps
compressibility     =  4.5e-5        ; compressibility of solvent used in
simulation in 1/bar
ref_p               =  160.0        ; reference P for coupling in bar

;        Velocity generation      Generate velocites is on at 300 K. Manual
gen_vel             =  yes        ; generate velocites according to Maxwell
distribution at T: gen_temp with random gen seed gen_seed
gen_temp            =  300.0        ; T for Maxwell distribution
gen_seed            =  173529        ; used to initialize random generator
for random velocities

;        Bonds
constraints         =  all-bonds    ; sets the LINCS constraint for all
constraint-algorithm = lincs

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