Hi Stephan,<br><br>It all a matter of time scale. Large molecules ==> slower movements (compare trucks and motor-bikes).<br><br>Cheers,<br>Itamar.<br><br><div class="gmail_quote">On 1 February 2011 03:18, lloyd riggs <span dir="ltr"><<a href="mailto:lloyd.riggs@gmx.ch">lloyd.riggs@gmx.ch</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear All,<br>
<br>
A quick question as I have not really delved into code for gromacs ever, nor know anyone close whom has worked on it.<br>
<br>
If I set up an MD simulation using a 4 protein complex, and 1 small peptide, plus waters, etc...and run the whole thing the proteins never move, only the amino acids within(constant temp RT and pressure 1 bar).<br>
<br>
Two domains make one complex, and another two the other. Basically, if I seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will drift (the chains) towards each other, but the two large (global) protein units never move their center (I know I can make it work with Pull vectors, but why not in the simple system with a generated initial randomized velocities), I woundered why they are fixed in a normal run with minimal parameters? Is there a reason (specific to developers), historical reason, or other? As waters move around fine, and anything else added (salt, small molecules of 20-30 atoms, water) except the central molecule(s) of interest.<br>
<br>
Grüsse<br>
<br>
Stephan Watkins<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br><br>-- <br><br><br>"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut<br><br>===========================================<br>
| Itamar Kass, Ph.D.<br>| Postdoctoral Research Fellow<br>|<br>| Department of Biochemistry and Molecular Biology<br>| Building 77 Clayton Campus<br>| Wellington Road<br>| Monash University,<br>| Victoria 3800<br>| Australia<br>
|<br>| Tel: +61 3 9902 9376<br>| Fax: +61 3 9902 9500<br>| E-mail: <a href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a><br>============================================<br>