Kavyashree M wrote:
Dear gromacs users,
I am trying to simulate a 225aa protein at 300K in water,
with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during
You're not doing NPT. You haven't specified pcoupl or any of the other relevant
parameters, so you're doing NVT.
position restrained md.
integrator = md
dt = 0.002
nsteps = 50000
nstcomm = 10
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.40
coulombtype = PME
rcoulomb = 1.40
vdwtype = Switch
rvdw_switch = 0.9
rvdw = 1.00
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl = nose-hoover
tc_grps = Protein Non-Protein
tau_t = 0.4 0.4
ref_t = 300 300
nh-chain-length = 1
gen_vel = no
continuation = yes
constraints = all-bonds
constraint-algorithm = LINCS
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
when I calculate the densities, the average came out to be 1025.91 kg/m^3,
Could anyone please clarify me the reason for this density.
Simulating with the right ensemble (NPT) will equilibrate the pressure and thus
density. As a fundamental point, please also realize that each water model has
its own (different) expected density value, which is also influenced somewhat by
the remaining contents of the system. Therefore, the result you obtain may not
be in exact agreement with experimental bulk density of water.
-Justin
Thanking you
With regards
Kavya
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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