<br><br><div class="gmail_quote">On Tue, May 15, 2012 at 11:26 AM, rama david <span dir="ltr"><<a href="mailto:ramadavidgroup@gmail.com" target="_blank">ramadavidgroup@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Gromacs Users ,<br> I simulated a 4 peptide in a box .<br> After completion of 30 ns simulattion , I extract <br>the particular time frame 29000 ps of my interest.<br> Now I want these frame for my next simulations <br>
study ..<br>In one simulation I want to keep the box size same as the <br>mentioned in extracted pdb and in another one I need to change the size of box to <br>70 70 70 <br><br><br>
REMARK GENERATED BY TRJCONV<br>
TITLE Protein in water t= 29000.00000<br>
REMARK THIS IS A SIMULATION BOX<br>
CRYST1 45.096 45.096 45.096 90.00 90.00 90.00 P 1 1<br>
MODEL 1<br>
<br> So my queries are like <br><br>1. Should I used the extracted frame directly for further study or <br> I need to remove the periodicity...??????<br></blockquote><div><br></div><div>I think its better to remove the periodicity when you are going to start a fresh simulation with this protein.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br> 2 . to change the box size how to proceed ??<br> Should I delete the line manually and adjust the box size????<br>
</blockquote><div><br></div><div>You can change the box dimensions with editconf using the -box (desired dimensions) option.</div><div> </div><div>-Anirban</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br><br>All suggestion are welcome ...<br><br><br>Than you in advance<span class="HOEnZb"><font color="#888888"><br><br>rama david <br> <br><br><br><br><br><br>
</font></span><br>--<br>
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