Thank you Justin, <br><br> When I went through most of the mailing list the fluctuations are not so high<br>and even in the FAQ it was mentioned in the range of 500-600 bar for 216 water.<br>And more over the average pressure was ~6bar instead of 1bar which was required.<br>
<br> So would you suggest that I can proceed with this file for the production run without<br>any problem. I was following your lysozyme tutorial where fluctuations were much <br>less.. hence I suspected some problem in this data.<br>
<br>Thanking you<br>With regards<br>M. Kavyashree<br><br><br><div class="gmail_quote">On Wed, Mar 16, 2011 at 8:52 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thank you Sir<br>
<br>
I am using OPLSAA with tip4p water model, I agree to the fact that<br>
it will oscillate but the oscillation is this case was from appr. -1000bar<br>
to 1000bar. And as it is stated in the FAQ regarding the variation of<br>
fluctuations with number of waters, this system has 6882 waters along<br>
with a protein of 123 aa, so is not this fluctuations high?<br>
</blockquote>
<br></div>
No. It is entirely expected, as you've been told. Also pay attention to this statement from the page linked before:<br>
<br>
"How much it varies and the speed at which it does depends on the type of pressure coupling used and the value of the coupling constants."<br>
<br>
You may not see the exact same behavior described on the Pressure page if you're using different settings.<br>
<br>
There is no problem here.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
Pressure coupling used -parinello-rahman<br>
tau_p = 2.0<br>
tau_t = 1.0<br>
compressibility 4.5e-5<br>
Pcouple_type = isotropic<br>
<br>
Any suggestions?<br>
<br>
Thanking you<br>
With Regards<br>
M. Kavyashree<br>
<br></div><div class="im">
On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a> <mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>> wrote:<br>
<br>
<br>
<br>
On 16/03/11, *Kavyashree M * <<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>>> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear users,<br>
<br>
Upon was trying to simulate an npt ensemble (protein in water),<br>
pressure was coupled using parinello rahman system with tau_p = 2,<br>
tau_t = 1; compressibility 4.5e-5, type = isotropic.<br>
<br>
(cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9;<br>
rcoulomb = 1.2; rlist = 1.2).<br>
<br>
No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3, 3.5),<br>
the pressure<br>
fluctuations are very drastic. I have gone through the mailing<br>
list regarding<br>
this issue but could not come to any conclusion.<br>
<br>
Any suggestions are helpfull.<br>
<br>
This is one of the statistics for pressure fluctuations.<br>
<br>
Statistics over 500001 steps [ 0.0000 through 1000.0000 ps ], 1<br>
data sets<br>
All statistics are over 100001 points<br>
<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Pressure 5.77629 0.99 398.013 -5.34218 (bar)<br>
</blockquote>
<br>
Looks very normal. See <a href="http://www.gromacs.org/Documentation/FAQs" target="_blank">http://www.gromacs.org/Documentation/FAQs</a><br>
number 3<br>
<br>
Mark<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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