Kavyashree M wrote:
I am sorry I did not include it in the mail: i used the following:
pcoupl = Parrinello_Rahman
pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
I agree that density of water is different depending on the model used,
so for tip4p water what is the range of fluctuations accepted? So that
we can conclude that the difference is not due to any other reason but
the water model used.
The extent of fluctuation in any pressure-related term depends on the size of
your system and several of the .mdp settings.
http://www.gromacs.org/Documentation/Terminology/Pressure
For the actual target value of TIP4P density, refer to the literature. The
TIP4P citation is provided in the Gromacs manual.
-Justin
Thanking you
With regards
Kavya
On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
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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