I am sorry I did not include it in the mail: i used the following:<br><br>pcoupl = Parrinello_Rahman <br>pcoupltype = isotropic <br>tau_p = 2.0 <br>
compressibility = 4.5e-5 <br>ref_p = 1.0 <br><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>Thanking you<br>With regards<br>Kavya<br><br><div class="gmail_quote">On Wed, Apr 13, 2011 at 5:38 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">
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>
</blockquote>
<br></div>
You're not doing NPT. You haven't specified pcoupl or any of the other relevant parameters, so you're doing NVT.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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 = 1 lincs-warnangle = 30 <br>
when I calculate the densities, the average came out to be 1025.91 kg/m^3,<br>
Could anyone please clarify me the reason for this density.<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanking you<br>
With regards<br>
Kavya<br>
<br>
</blockquote>
<br></div>
-- <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>
<br>
========================================<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote></div><br>