Yes, you are right. I didn't apply pressure coupling and my simulation is under NVT. <br>I just want to get the density of water vs time . Thanks so much . <br><br>-Xianghong Qi<br><br><div class="gmail_quote">On Wed, Nov 5, 2008 at 4:32 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d"><br>
<br>
Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
xianghong qi wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks, Justin:<br>
<br>
I use 4.0. Mine is here:<br>
-------------------------------------------------------------------<br>
1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 9 Pressure-(bar) 10 Vir-XX 11 Vir-XY 12 Vir-XZ 13 Vir-YX 14 Vir-YY 15 Vir-YZ 16 Vir-ZX 17 Vir-ZY 18 Vir-ZZ 19 Pres-XX-(bar) 20 Pres-XY-(bar)<br>
21 Pres-XZ-(bar) 22 Pres-YX-(bar) 23 Pres-YY-(bar) 24 Pres-YZ-(bar)<br>
25 Pres-ZX-(bar) 26 Pres-ZY-(bar) 27 Pres-ZZ-(bar) 28 #Surf*SurfTen<br>
29 Mu-X 30 Mu-Y 31 Mu-Z 32 T-System<br>
</blockquote></blockquote></blockquote>
<br></div>
...and I really should not hit "send" until I'm done thinking. Are you applying pressure coupling in your simulation? Under NVT conditions, parameters like Volume and Density are not written, since volume is constant and density doesn't mean much without constant pressure.<div>
<div></div><div class="Wj3C7c"><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
-Xianghong Qi<br>
<br>
On Wed, Nov 5, 2008 at 4:20 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>
xianghong qi wrote:<br>
<br>
Hello, all:<br>
<br>
I checked the mailing list. Looks like g_energy can calculate<br>
density vs time, but<br>
my g_energy doesn't have options like density, volume? I am<br>
wondering how I can<br>
get my density vs time graph? Any suggestion is appreciated.<br>
Thanks.<br>
<br>
<br>
Look more closely. Both versions of Gromacs that I am currently<br>
using (3.3.3 and 4.0) have options for Density, Volume, and Box<br>
vectors as output from g_energy.<br>
<br>
-Justin<br>
<br>
<br>
-Xianghong Qi<br>
<br>
<br>
<br>
-- Some people make the world more special just by being in it.<br>
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========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<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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