Dear Cesar,<br>Thank you for your reply,<br><br>There are two different kind of water gro in this site (one of them is water.gro in :<br><a href="http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html">http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html</a> <br>
and another is water-1bar-303k.gro in :<br> <a href="http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html">http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html</a> . Is there difference between them? <br>Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script?<br>
<br>Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it.<br>
<br>Cheers<br>Rasoul <br><br><br><div class="gmail_quote">On Fri, Dec 18, 2009 at 9:02 PM, César Ávila <span dir="ltr"><<a href="mailto:clavila@gmail.com">clavila@gmail.com</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;">
For a detailed description of how to set up protein simulation, I recommend you to read the Martini Tutorial on <br><a href="http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html" target="_blank">http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html</a><br>
there you will find step by step instructions along with some explanations of what you are actually doing. <br>In this case you only want to build a water box around your protein. For that you will use editconf and a vdw distance of 0.19. <br>
<br>Regards<br>Cesar<br><br><div class="gmail_quote"><div><div></div><div class="h5">2009/12/17 rasoul nasiri <span dir="ltr"><<a href="mailto:nasiri1355@gmail.com" target="_blank">nasiri1355@gmail.com</a>></span><br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">yes, I know there will be limitation for modeling of Folding/Unfolding proteins with MARtini CGFF if I want to look at complete folding/unfolding mechanism of proteins but I want to find out localized regions of the protein (e.g. the C- or N-termini) that they have contribution to the denaturation mechanism.<br>
My question is about vdwd in beads of water. Is it OK if I select distances of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to reconstruct the system in smaller vdw distance of the water beads for doing my purpose. and Which commands of Gromacs can do it? <br>
<br>Best regards<br><font color="#888888">Rasoul <br><br></font><div class="gmail_quote"><div><div></div><div>On Thu, Dec 17, 2009 at 5:03 PM, César Ávila <span dir="ltr"><<a href="mailto:clavila@gmail.com" target="_blank">clavila@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div>
I suggest you read the original paper for Martini Protein FF. I think it is not suitable for your purpouse. <br><br><div class="gmail_quote">2009/12/17 rasoul nasiri <span dir="ltr"><<a href="mailto:nasiri1355@gmail.com" target="_blank">nasiri1355@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div>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>
<font color="#888888">
<br>Rasoul</font><div><div></div><div><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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