Hi,<br><br>My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs.<br>I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the smaller radius of van der waals of the water beads, then I will continue CGMD simulation. Is it possible I reduce this radius? Which commands of Gromacs suit can do it? <br>
<br>Rasoul<br><br><div class="gmail_quote">On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">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>rasoul nasiri wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
greetings GMX users,<br>
<br>
When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? <br>
</blockquote>
<br></div>
Read up on your forcefield and find out how "large" the particles tend to be. It only has to be good enough, not perfect.<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I have to switch back to the smaller radius afterward, Is it correct? <br>
</blockquote>
<br></div>
Changing what for what purpose?<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
if yes, How can I do it? I tried with editconf but could not.<br>
</blockquote>
<br></div>
I don't know what you mean.<br>
<br>
Mark<br><font color="#888888">
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