<span class="q" id="q_113d343b93afca2b_1"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">------------------------------<br><br>Message: 5<br>
Date: Mon, 16 Jul 2007 16:39:29 +0200<br>From: "Jeroen van Bemmelen" <<a href="mailto:J.J.M.vanBemmelen@tnw.tudelft.nl" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
J.J.M.vanBemmelen@tnw.tudelft.nl</a>><br>Subject: [gmx-users] Regarding polymer equillibration (pressure<br> changes)<br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:469B9F40.30804.32BEF5D@J.J.M.vanBemmelen.tnw.tudelft.nl" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
469B9F40.30804.32BEF5D@J.J.M.vanBemmelen.tnw.tudelft.nl</a>><br>Content-Type: text/plain; charset=US-ASCII<br><br>Hi Ann,<br><br>> So my first question is<br>><br>> wether this can be possible or not? or am I doing something wrong?
<br>> if so, then how can i rectify the same error?<br><br>I think you should definitely use 'editconf -density' to rescale your<br>simulation box to the right density. editconf automatically rescales<br>the box vectors AND the coordinates, so you won't have the problem of
<br>atom coordinates suddenly being larger than the box vectors.<br><br>But anyhow it seems a bit weird to me that you're coordinates are so<br>much larger than your box vectors (4.3 versus 3.4 nm). Perhaps this<br>is related to the long molecule chains in combination with pbc? I'm
<br>not sure, maybe one of the developers can comment on this.<br><br><br>> I think the fluctuations are okay and admittable.but the change in pressure<br>> averages make me confused.<br>><br>> If I am right, at equillibrium all the observables (temp, pressure, density)
<br>> should average around a steady value with some fluctuations. but the change<br>> in averages (pressure) makes me confused. I have read from literature that<br>> the equillibriation of polymers is comparitively diffcult.
<br><br>Fluctuations in the average pressure do not necessarily mean there's<br>a equilibration problem, depending on the time it takes for the<br>average pressure to converge for your system. Simply a matter of<br>statistics.
<br><br>Since the pressure is always fluctuating enormously and converging<br>slowly compared to other observables, I don't think that (only)<br>checking the average pressure is a good way of determining whether a<br>
system is equilibrated or not. Of course, a drift in the average<br>pressure could mean that your system is not equilibrated. But in that<br>case you'd probably also see a significantly large drift in other<br>observables, especially the potential energy and partial potential
<br>energy terms in your case.<br><br>Cheers,<br>Jeroen</blockquote></span><div><br><br><br><br>Hi jeroen <br><br>Thank
you for the reply. I forgot to mention the avergae potential , kinetic
and total energy for the simulation runs are as follows
<br><br>###############################################################################################################<br>5ns NPT simulation <br><br><br>Last frame read 10000 time 5000.000<br><br></div><br>Statistics over 5000001 steps [
0.0000 thru 5000.0000 ps ], 1 data sets<br>
<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>
------------------------------<div>-------------------------------------------------<br>
Total-Energy 4331.96 355.493 355.355 0.00685523 34.2761<br>
<br>Potential energy -9401.33 250.37 250.31 0.00378263 18.9132<br><br>Kinetic energy 13733.3 235.6 235.558 0.0030726 15.363 <br><br>Pressure 10.4371
724.216 724.216 -8.51094e-05 -0.425347 <br><br>Temperature 450 7.71993 7.71856 0.0010068 34.2761<br><br>Density 916.781 6.60382 6.60252 9.09303e-05
0.454652<br><br>##################################################################################################<br><br>5ns NVT simulation <br>
<br>
<br>
Last frame read 10000 time 5000.000<br>
<br>
<br>
Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 1 data sets<br>
<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Total-Energy 4335.29 352.244 351.929 0.0103137 51.5683<br>
<br>
Potential energy -9397.99 244.804 244.693 0.00509701 25.4881<br>
<br>
Kinetic energy 13733.3 236.317 236.197 0.00521605 26.0803 <br>
<br>
Pressure 18.06 802.822 802.807 -0.00349252 -17.4726 <br>
<br>
Temperature 450 7.74343 7.7395 0.000170915 0.854575<br>
<br>
Density 927.262 (g_density -f traj.xtc -s ppo.tpr -sl 1) <br>
<br>#######################################################################################################<br>
<br>10ns NVT simulation <br>
<br>
<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Total-Energy 4339.31 350.971 350.812 -0.00732073 -36.6037<br>
<br>
Potential energy -9393.97 244.091 243.963 -0.0054728 -27.3624<br>
<br>
Kinetic energy 13733.3 236.317 236.197 0.00521605 26.0803 <br>
<br>
Pressure 28.5734 801.629 801.56 0.00729491 39.4746<br>
<br>
Temperature 450 7.73025 7.72976 -6.05616e-05 -0.302808<br>
<br>
Density 927.263 (g_density -f traj.xtc -s ppo.tpr -sl 1) <br>
<br>
########################################################################################################<br><br><br>The
above mentioned are the averages for the system in the cubical box
where the coordinates have vallues greater than the box length.
<br>One of my question was left unanswered regarding the calculation of density. <br><br>1.Can
i use (g_density -f traj.xtc -s ppo.tpr -sl 1) to calculate the density
of the system in NVT simulation? are the options correct to calculate
the density?
<br><br>2. When I view the trajectories (ngmx -f traj.xtc -s top.tpr)
of my run i always found my polymer chains hanging out of the box.Is it
the periodic boundary condition that i observe in veiwing the
trajectory? (as i mentioned before some of my cordinates are greater
than box length). is that can be the reason for the same?
<br><br>3. How can i keep all my molecules inside the box during the simulation run? <br><br><br><br><br><br>Thanking you in advance<br><br></div>