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> 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 class="gmail_quote">On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</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><div></div><div class="h5"><br><br><span>On 16/03/11, <b>Kavyashree M </b> <<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>> wrote:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>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), the pressure<br>fluctuations are very drastic. I have gone through the mailing 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 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)</div>
</blockquote><br></div></div>Looks very normal. See <a href="http://www.gromacs.org/Documentation/FAQs" target="_blank">http://www.gromacs.org/Documentation/FAQs</a> number 3<br><font color="#888888"><br>Mark
</font><br>--<br>
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