[gmx-users] Regarding polymer equillibration (pressure changes )

[ann rose]

Hi Gromacs crew and others

I have a few questions regarding the equilibration of the system
my system is linear PPG (polyprpylene glycol)polymer chain (melts in vaccum)
with the following details

number of monomers = 22
Total number of atoms = 3664
total number of chains = 16

My chains are aranged in  a cubical box and growing along the y axis
(crystal)with an initial box length of 10 10 10 along the three axes.
Then I perfored a 0.5ns  NPT simulation with the mdp parameters as follows

integrator               = md
dt                       = 0.001
nsteps                   = 500000
comm_mode                = linear
nstcomm                  = 1
nstxout                  = 10000
nstvout                  = 10000
nstfout                  = 0
nstlog                   = 500
nstenergy                = 500
nstxtcout                = 10000
xtc_precision            = 10000
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 0.9
coulombtype              = PME
rcoulomb                 = 0.9
fourierspacing           = 0.1
pme_order                = 4
ewald_rtol               = 1e-5
optimize_fft             = yes
vdwtype                  = cut-off
rvdw                     = 1.2
tcoupl                   = nose-hoover
tc-grps                  = system
tau_t                    = 0.5
ref_t                    = 450
Pcoupl                   = berendsen
pcoupltype               = isotropic
tau_p                    = 2.0
compressibility          = 4.5e-5
ref_p                    = 650.0
annealing                = no
gen_vel                  = no
gen_temp                 = 500
gen_seed                 = 173529
morse                    = no
constraints              = none
constraint_algorithm     = lincs
unconstrained_start      = no
lincs_order              = 4
lincs_iter               = 1


Avergaes over the run were as follows with fluctuations

pressure  = 355.327 (fluctutaion = around 700)
Temperature = 450.001
density = 659.956
box length = 3.31199

Then I performed a 5ns NPT simulation with the above parametes in mdp file
but with change in ref_p as 10bar. The averges afer the run were as follows
with fluctuations

pressure  = 10.4371 (fluctutaion = around 700)
Temperature = 450
density = 916.781
box length = 3.36644 (final gro file)

Then i switched over to 5ns NVT by switching off the pressure coupling. As
the box lenght was fluctuating i took the average of box lenghth (3.37275)and
manually edited the final gro file from the NPT run and performed the NVT
simulation. But there were some (MANY) coordinates that were greater than
the above boxlength. as given below

   PPG   H340 2433   4.174   2.456   0.903  1.8080  1.7019 -0.2709
   PPG   H341 2434   4.274   2.476   1.047 -1.0495 -1.9389  2.3833
   PPG   H342 2435   4.140   2.591   1.014

 So my first question is

 wether this can be possible or not? or am I doing something wrong?
 if so, then how can i rectify the same error?

The averages after the run were as follows

pressure  = 18.06  (fluctutaion = 802.807)
Temperature = 450
density = 927.262  (calculated using "g_density -f traj.xtc -s NVT_5ns.tpr
-sl 1")
box length = 3.37275 (final gro file)

is the g_density command as given in the brackets will give the correct
density of my system ? if no, then what is the option that i have to set for
the same ?

Is the change in pressure and density okay? or is there something going
wrong?

Then i extended the above NVT simulation to 5ns more to observe the change
in energy averages and was found to be as follows


pressure  = 28.5734  (fluctutaion = 802.807)
Temperature = 450   (fluctutaion = 7.72976)
density = 927.263  (calculated using "g_density -f traj.xtc -s NVT_10ns.tpr
-sl 1")
box length = 3.37275 (final gro file)

why there can be an increase in pressure? does that means that my system is
not equilibriated?  if so how can i make my system at equillibrium?

I think the fluctuations are okay and admittable.but the change in pressure
averages make me confused.


If I am right, at equillibrium all the observables (temp, pressure, density)
should average around a steady value with some fluctuations. but the change
in averages (pressure) makes me confused. I have read from literature that
the equillibriation of polymers is comparitively diffcult.


Thanking you in advance
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