I am sorry.My system does not explode. It just kind of fuses. The atoms come close together and form a rounded mass.<br>
-<br>
karamyog.<br><br><div><span class="gmail_quote">On 5/29/06, <b class="gmail_sendername">karamyog singh</b> <<a href="mailto:karamyog.singh@gmail.com">karamyog.singh@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>However if the gen_velocity breaks up my system and at the end of my
simulation, I do not get a bcc structure at lets say 273 K, which I am
not getting, then how can I consider my simulation to be correct? The
structure should remain the same. Or could it be that since my
structure is a nano layer film, therefore it is unstable and explodes
and I should not compare my results with a bulk material?<br>
<br>
Moreover, to avoid the error in the LJ, I have changed my system to
copper and have used the potential parameters given in gromacs.
Temperature of simulation is 273 and I have used the option no for
Pressure coupling because i want my system to be at 1 bar.<br>
-<br></div><div><span class="sg">
karamyog.</span></div><div><span class="e" id="q_10b7f44e48092f77_2"><br><br><div><span class="gmail_quote">On 5/29/06, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
Mark.Abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
karamyog singh wrote:<br>> Does this give any clue. It shows large PE, KE and temp. Could that be a<br>> reason? More information required?<br><br>Your PE is ridiculously large. You have order 10^5 kJ/mol of PE for
<br>
every atom, and obviously that is only coming from your LJ function.<br>Check how you generated that and told gromacs what it should be. Be<br>careful of units and multiples of 1000! In the absence of temperature<br>control, that PE will equipartition to the KE degrees of freedom,
<br>leading to the other observations of high KE and temperature.<br><br>> However, I have chenged my system a bit. My conf.gro file has just 2<br>> atoms. one at the origin and the other at the body center. I use genconf
<br>> to create a mesh of 4x4x4 unit cells at a distance of 0 0 0. I thought<br>> this is a better way to simulate a set of crystals.<br><br>Sounds like a better way to generate your simulation cells. You<br>shouldn't now have overlapping atoms (check the output .gro file
<br>yourself) but you will have a simulation cell that is initially<br>symmetric, until the gen_vel random KE breaks it.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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</span></div></blockquote></div><br>