<div>Dear List and Mark</div><div>I followed your suggestions equilibrating the proteins of my complex separately. In both cases i'm able to correctly equilibrate the system and to perform a short md of 500ps. So I suppose that when i simulate both protein together somewhere there is a clash. Now how could I highlight the problem? In your opinion the clash could be more probably due to solvent molecules or to my proteins perhaps too near each other?</div>
<div>Thank you very much</div><div>Guido<br><div><br><div class="gmail_quote">2012/1/11 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5">On 11/01/2012 8:35 PM, Guido Leoni wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear List<br>
I'm newbie to gromacs (sigh). I'm simulating the interaction between two proteins(chrystallographic structures) following the spider toxin tutorial. I'm able to correctly minimize ( E<1000) and equilibrate (400 ps ) the system. No error message appears to me and I'm quite sure that my starting structures have no steric clashes.<br>
My .mdp files are equal to the tutorial description excepted for the choosen timesteps (400 ps in equilibration and 1000 ps in dynamics).<br>
When I run the dynamic (launching gromacs with mpi) I retrieve after 7 ps the following error message<br>
"2 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group"<br>
I suppose that this is due to the energy of some components that blow up.<br>
Please how can i check which components are responsible for the problem?<br>
I'm also looking the instruction on the web site but they appear to me a bit cryptic. For example<br>
<br>
If the crash is happening relatively early (within a few steps), set nstxout (or nstxtcout) to 1, capturing all possible frames. Watch the resulting trajectory to see which atoms/residues/molecules become unstable first.<br>
<br>
I looked the resulting trajectories of the 2 proteins with ngmx but they seem to be always in the box and it is impossible to graphically check the water molecules .<br>
<br>
</blockquote>
<br></div></div>
The next piece of advice is to simplify your problem. If you can get each of your proteins to equilibrate on their own, then you probably have an atomic clash after all. If one doesn't equilibrate, then maybe your simulation conditions or topology is suspect.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Guido Leoni<br>National Research Institute on Food and Nutrition<br>(I.N.R.A.N.)<br>via Ardeatina 546<br>00178 Rome<br>Italy<br><br>tel + 39 06 51 49 41 (operator)<br>
+ 39 06 51 49 4498 (direct)<br>
</div></div>