The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)<br>stated a density of 0.999g/cc at 298K and 1atm, which is nowhere<br>close to the value i have got. (1.025g/cc). or is this value tolerable?<br><br><br><div class="gmail_quote">
On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I am sorry I did not include it in the mail: i used the following:<br>
<br>
pcoupl = Parrinello_Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 <br>
I agree that density of water is different depending on the model used,<br>
so for tip4p water what is the range of fluctuations accepted? So that<br>
we can conclude that the difference is not due to any other reason but<br>
the water model used.<br>
<br>
</blockquote>
<br></div>
The extent of fluctuation in any pressure-related term depends on the size of your system and several of the .mdp settings.<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Pressure" target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
<br>
For the actual target value of TIP4P density, refer to the literature. The TIP4P citation is provided in the Gromacs manual.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Thanking you<br>
With regards<br>
Kavya<br>
<br></div><div><div></div><div class="h5">
On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Kavyashree M wrote:<br>
<br>
Dear gromacs users,<br>
I am trying to simulate a 225aa protein at 300K in water,<br>
with OPLSAA force filed, tip4p water model, using the<br>
parameters below (for pressure equilibration) during<br>
<br>
<br>
You're not doing NPT. You haven't specified pcoupl or any of the<br>
other relevant parameters, so you're doing NVT.<br>
<br>
<br>
position restrained md.<br>
<br>
integrator = md dt = 0.002 nsteps = 50000 nstcomm = 10 nstlist = 5 ns_type = grid pbc = xyz rlist = 1.40<br>
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<br>
tau_t = 0.4 0.4 ref_t = 300 300 nh-chain-length = 1 gen_vel = no continuation = yes constraints = all-bonds<br>
constraint-algorithm = LINCS<br>
lincs-order = 4 lincs-iter =<br>
1 lincs-warnangle = 30<br>
when I calculate the densities, the average came out to be<br>
1025.91 kg/m^3,<br>
Could anyone please clarify me the reason for this density.<br>
<br>
<br>
Simulating with the right ensemble (NPT) will equilibrate the<br>
pressure and thus density. As a fundamental point, please also<br>
realize that each water model has its own (different) expected<br>
density value, which is also influenced somewhat by the remaining<br>
contents of the system. Therefore, the result you obtain may not be<br>
in exact agreement with experimental bulk density of water.<br>
<br>
-Justin<br>
<br>
<br>
Thanking you<br>
With regards<br>
Kavya<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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