Thank you Justin!<br><br><div class="gmail_quote">On Wed, Mar 16, 2011 at 9:28 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 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>
</blockquote>
<br></div>
You cannot always assume that rules of thumb and others' results will (or should) necessarily match your own. Unless you are using identical input files, you won't necessarily get the same results. Much of the fluctuation information is probably based on the Berendsen thermostat, which does not oscillate as much as Parrinello-Rahman. Other factors in the .mdp file will influence these statistics, since both the kinetic energy of the system and the virial are used to calculate pressure (see the manual).<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
And more over the average pressure was ~6bar instead of 1bar which was required.<br>
<br>
</blockquote>
<br></div>
And with fluctuations +/- 1000, is 6 really all that different from 1? There was an extensive discussion some time back about this. I would suggest you have a look through the archive.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
</blockquote>
<br></div>
The lysozyme system has nearly twice the number of waters that your system has (over 10,000), hence the fluctuations will be much smaller, and even then, the pressure oscillates by +/- 400 or so.<br>
<br>
Again, I see no problem here. What you report is what is to be expected.<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">
Thanking you<br>
With regards<br>
M. Kavyashree<br>
<br>
<br></div><div><div></div><div class="h5">
On Wed, Mar 16, 2011 at 8:52 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>
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<br>
appr. -1000bar<br>
to 1000bar. And as it is stated in the FAQ regarding the<br>
variation of<br>
fluctuations with number of waters, this system has 6882 waters<br>
along<br>
with a protein of 123 aa, so is not this fluctuations high?<br>
<br>
<br>
No. It is entirely expected, as you've been told. Also pay<br>
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<br>
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<br>
page if you're using different settings.<br>
<br>
There is no problem here.<br>
<br>
-Justin<br>
<br>
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>
On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham<br>
<<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>><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a><br>
<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>
<mailto:<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a> <mailto:<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>>>> wrote:<br>
<br>
Dear users,<br>
<br>
Upon was trying to simulate an npt ensemble (protein in<br>
water),<br>
pressure was coupled using parinello rahman system with<br>
tau_p = 2,<br>
tau_t = 1; compressibility 4.5e-5, type = isotropic.<br>
<br>
(cut off scheme (vdw_type = switch; rvdw = 1.0;<br>
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,<br>
3.5),<br>
the pressure<br>
fluctuations are very drastic. I have gone through the<br>
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<br>
ps ], 1<br>
data sets<br>
All statistics are over 100001 points<br>
<br>
Energy Average Err.Est. RMSD<br>
Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Pressure 5.77629 0.99 398.013<br>
-5.34218 (bar)<br>
<br>
<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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Justin A. Lemkul<br>
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Virginia Tech<br>
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-- <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>
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