Kavyashree M wrote:
The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc). or is this value tolerable?
That's a 2.6% difference. I wouldn't call that "nowhere close." Unless you are
literally reproducing the exact same system used during parameterization (which
you're not, based on your system contents and the use of algorithms like PME
that didn't exist in 1983) then you shouldn't necessarily expect identical results.
-Justin
On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> 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> <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 <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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