Thank you Mark, for your answer.<br>This time I have another issue: temperature.<br>What are the ways to control temperature in gromacs (during heating or equilibration phases), other than temperature coupling?<br><br>Thank you<br>
Carla<br><br><div class="gmail_quote">On Thu, Jan 14, 2010 at 10:40 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density.<br>
</blockquote>
<br></div>
Those tools report density-related quantities, they do not control it.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
However, when I use g_energy, in my list, "Density" doesn't appear.<br>
</blockquote>
<br></div>
g_energy doesn't report the density if you have a constant-volume simulation (but grompp probably reported it when you generated the .tpr)<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Else, if I use g_density, it needs a file traj.xtc which I don't have.<br>
</blockquote>
<br></div>
Per Erik's point, you can usually use any coordinate file or trajectory file.<br><font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
So please can anyone tell me how to check my system's density in gromacs?<br>
<br>
Thank you<br>
<br>
Carla<br>
<br>
</blockquote></div><div><div></div><div class="h5">
-- <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/search" target="_blank">http://www.gromacs.org/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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>