I know where the minimum is and I said exactly what you did. However I
interpreted the potential becoming 0 as the point before r-min. The
potential once becomes 0 before minimum potential value. I thought you
were referring to that point and that is why i got confused and asked
you further questions.<br>
<br>
anyway, thanks a lot for your help. Hope I get my desired result. :) Thanks a lot!<br><br><div><span class="gmail_quote">On 5/18/06, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">
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>> I placed the atoms randomly means i used random atomic positions, not
<br>> velocities. The velocities were 0 initially and then I generated<br>> velocities at 0.01 K.(1st MD run to get a stable configuration) After<br>> that I subjected this structure that I got to NVE.(2nd MD run) Now over
<br>> here I will try with no velocity generation. Thank you for pointing out<br>> this mistake. I should have realised this. One more thing, is generating<br>> velocities in the MD run correct?<br><br>It isn't meaningful to have velocities before starting an MD run, so you
<br>want to generate them at some point before any MD, then equilibrate as<br>appropriate.<br><br>> I will try what you are saying. I was doing it till the r-min beacuse at<br>> that point the forces become 0.Minimum
potential should imply 0 force.<br>> So if the forces are zero and I increase my simulation time for 1st MD<br>> run, I get a stabler structure i.e. the forces between atoms should be<br>> nearly equal to zero. However my forces wil never be zero. Wil I ever
<br>> get a frozen structure for NVE?<br><br>The minimum of the potential is where -F=dU/dx=0, not where U=0 - after<br>all the latter depends where you take your convention of zero energy. A<br>normal (e.g. 6,12) LJ potential has a minimum below zero and then
<br>converges up to it (e.g. Fig 4.1 in gromacs manual). You want your<br>cutoff to be large enough that your potential is getting close to zero<br>under the standard convention that zero is at infinite separation -<br>because the cutoff means that the potential effectively is zero. My
<br>point is that a cut-off at the minimum gives you a sharp discontinuity<br>for your effective potential, which means you are doing something other<br>than you want to do.<br><br>Mark<br><br></blockquote></div><br>