David, <div>thank you for your reply. </div><div><div><br></div><div>but, g_msd gives a diffusion coefficient which is one order of magnitude higher than expected for a small polypeptide (15 res long with gyration Rg ~ 0.8nm) with the same size. this is command line i used: </div>
<div>g_msd-mpi -f md_mine_2nd.xtc -s md_mine_2nd.tpr -o msd_2nd.xvg</div><div><br></div><div>when visualizing, I can see that the polypeptide crosses the boundary several times. apparently, g_msd counts these 'artificial' jumps in MSD calculation. and, that's probably why the diffusion coefficient is calculated such high (i.e. 500 um2/s for a small protein). </div>
<div><br></div><div>if this is the case, it is a bug in g_msd I believe. </div><div><br></div><div>is there any way to get round this problem?</div><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Anonymous</b> <span dir="ltr"><<a href="mailto:rossen@kth.se">rossen@kth.se</a>></span><br>
Date: Fri, Dec 9, 2011 at 12:17 AM<br>Subject: Comment for Forum topic: diffusion coefficient<br>To: <a href="mailto:ruhollah.mb@gmail.com">ruhollah.mb@gmail.com</a><br><br><br>Hi ruhollahmoussavi-baygi,<br>
<br>
Comment by davidvanderspoel: diffusion coefficient<div class="im"><br>
<br>
On 2011-12-09 08:34, Mark Abraham wrote:<br>
> On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote:<br>
>> I want to calculate the diffusion coefficient of a small polypeptide<br>
>> with g_msd (see here<br>
>> <a href="http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/<u></u>Diffusion_Constant</a> [1])<br>
>><br>
>> because of periodic boundary condition, when the peptide goes out of<br>
>> the right side it comes in from left side, which leads to an<br>
>> artificial displacement. this will give rise to a non-realistic MSD.<br>
>><br>
>> is g_msd intelligent enough to avoid this artificial displacement?<br>
>><br>
><br></div>
Yes it is.<div class="im"><br>
<br>
> Not sure about g_msd, but you can take care of it yourself with a<br>
> workflow derived from the information here<br>
> <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condi." target="_blank">http://www.gromacs.org/<u></u>Documentation/Terminology/<u></u>Periodic_Boundary_Condi.</a>.. [2]<br>
><br>
><br>
> Mark<br>
<br></div>
Read more <a href="http://support.scalalife.eu/content/diffusion-coefficient#comment-103" target="_blank">http://support.scalalife.eu/<u></u>content/diffusion-coefficient#<u></u>comment-103</a><div class="HOEnZb"><div class="h5">
<br>
<br>
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<br>
[1] <a href="http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/<u></u>Diffusion_Constant</a><br>
[2] <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/<u></u>Documentation/Terminology/<u></u>Periodic_Boundary_Conditions</a><br>
<br>
</div></div></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Ruhollah Moussavi-Baygi<br>
</div>