[gmx-users] Reg: NPT Equilibration of water

[vinothkumar mohanakrishnan]

Hi Gromacians

I want to do equilibration of water (spc model) first in the NVT ensemble
and then in the NPT ensemble to maintain a temperature of 300K and a
pressure of 1 bar respectively. The NVT equilibration works fine and the
average temperature turns out to be 299.229 K.

Energy                      Average       RMSD        Fluct.
Drift            Tot-Drift
------------------------------
-------------------------------------------------
Temperature                 299.229    10.3092    10.2463  0.0393873
3.93877
Heat Capacity Cv:       12.494 J/mol K (factor = 0.00118698)

 when i do NPT equilibration i am not getting the desired pressure as 1 bar
or atleast close to 1 bar (between 1-1.4 bar). In the mdp file i used
semiisotropic pressure coupling type because i want to fix the length of the
box same on two axis as that of the original box size and want to change it
only on one axis. can any one tell me why iam not getting the desired
pressure of 1 bar?.

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Pressure (bar)               7.4339    574.052    573.574   0.812129
81.2138

Given below is my mdp file (NPT equilibration). any help is highly
appreciated.

title           = DCE NVT equilibration
cpp           = usr/bin/cpp
integrator   = md
nsteps       = 100000
dt              = 0.001
nstxout       = 100
nstvout       = 100
nstenergy   = 100
nstlog        = 100
ns_type     = grid
nstlist        = 1
rlist            = 1.0
coulombtype    = PME
rcoulomb         = 1.0
vdwtype          = Cut-off
rvdw               = 1.0
pme_order       = 4
fourierspacing  = 0.16
pbc                 = xyz
tcoupl              = V-rescale
tc-grps             = system
tau_t                = 0.1
ref_t                 = 300
pcoupl              = berendsen
pcoupltype        = semiisotropic
tau_p                = 0.5
ref_p                 = 1.0 1.0
compressibility   = 0.0 4.5e-5
DispCorr            = Enerpres
gen_vel             = yes
gen_temp          = 300
gen_seed          = 173529

Regards
Vinoth
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