what is yr real prob tell me?<br><br><br><div class="gmail_quote">On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Quoting chandrabhan seniya <<a href="mailto:chandrabhanseniya@gmail.com">chandrabhanseniya@gmail.com</a>>:<br>
<br>
> no prob you wait for some time it will write topology file and the proceed<br>
> further..<br>
<br>
I think that a lipid molecule trying to tear itself apart at step 0 would fall<br>
under the category of a "problem," and it will not disappear on it's own if we<br>
conveniently ignore it...<br>
<br>
><br>
> On Thu, Apr 24, 2008 at 5:04 PM, <<a href="mailto:gadies@fh.huji.ac.il">gadies@fh.huji.ac.il</a>> wrote:<br>
><br>
> > Hi,<br>
> ><br>
> > The full mdrun output when the simulation blows up is:<br>
> ><br>
> > Step 0, time 0 (ps) LINCS WARNING<br>
> > relative constraint deviation after LINCS:<br>
> > max inf (between atoms 6 and 7) rms inf<br>
> > bonds that rotated more than 30 degrees:<br>
> > .<br>
> > .<br>
> > .<br>
> > Warning: 1-4 interaction between 1 and 6 at distance<br>
> > 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm<br>
> > These are ignored for the rest of the simulation<br>
> > This usually means your system is exploding,<br>
> > if not, you should increase table-extension in your mdp file<br>
> ><br>
> > Thanks Gadi<br>
> ><br>
> > Quoting "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>:<br>
> ><br>
> ><br>
> > > Did your minimization converge to a nice, negative potential energy?<br>
> > > Also, what<br>
> > > is the full mdrun output when the simulation blows up? You've quoted<br>
> > > the last<br>
> > > bit, but it would be more informative to see the whole output, or at<br>
> > > least a<br>
> > > description of it (i.e., LINCS warnings).<br>
> > ><br>
> > > -Justin<br>
> > ><br>
> > > Quoting <a href="mailto:gadies@fh.huji.ac.il">gadies@fh.huji.ac.il</a>:<br>
> > ><br>
> > ><br>
> > > > Hi,<br>
> > > ><br>
> > > > I tried using no temperature coupling and no constraints, that did not<br>
> > > > help.<br>
> > > > If I run the simulation without the position restraints it works OK.<br>
> > > > Could there by something wrong with the posre file (I'll attach it at<br>
> > > > the end of the email).<br>
> > > > I want one of the atoms in the lipid to stay in one place and the rest<br>
> > > > to wiggle around it. Is there any other way to do that which is not<br>
> > > > position restraints.<br>
> > > ><br>
> > > > Thanks Gadi<br>
> > > ><br>
> > > ><br>
> > > > [ position_restraints ]<br>
> > > > ; atom type fx fy fz<br>
> > > > 1 1 0 0 0<br>
> > > > 2 1 0 0 0<br>
> > > > 3 1 0 0 0<br>
> > > > 4 1 0 0 0<br>
> > > > 5 1 0 0 0<br>
> > > > 6 1 0 0 0<br>
> > > > 7 1 0 0 0<br>
> > > > 8 1 1000.0 1000.0 1000.0<br>
> > > > 9 1 0 0 0<br>
> > > > 10 1 0 0 0<br>
> > > > 11 1 0 0 0<br>
> > > > 12 1 0 0 0<br>
> > > > 13 1 0 0 0<br>
> > > > 14 1 0 0 0<br>
> > > > 15 1 0 0 0<br>
> > > > 16 1 0 0 0<br>
> > > > 17 1 0 0 0<br>
> > > > 18 1 0 0 0<br>
> > > > 19 1 0 0 0<br>
> > > > 20 1 0 0 0<br>
> > > > 21 1 0 0 0<br>
> > > > 22 1 0 0 0<br>
> > > > 23 1 0 0 0<br>
> > > > 24 1 0 0 0<br>
> > > > 25 1 0 0 0<br>
> > > > 26 1 0 0 0<br>
> > > > 27 1 0 0 0<br>
> > > > 28 1 0 0 0<br>
> > > > 29 1 0 0 0<br>
> > > > 30 1 0 0 0<br>
> > > > 31 1 0 0 0<br>
> > > > 32 1 0 0 0<br>
> > > > 33 1 0 0 0<br>
> > > > 34 1 0 0 0<br>
> > > > 35 1 0 0 0<br>
> > > > 36 1 0 0 0<br>
> > > > 37 1 0 0 0<br>
> > > > 38 1 0 0 0<br>
> > > > 39 1 0 0 0<br>
> > > > 40 1 0 0 0<br>
> > > > 41 1 0 0 0<br>
> > > > 42 1 0 0 0<br>
> > > > 43 1 0 0 0<br>
> > > > 44 1 0 0 0<br>
> > > > 45 1 0 0 0<br>
> > > > 46 1 0 0 0<br>
> > > > 47 1 0 0 0<br>
> > > > 48 1 0 0 0<br>
> > > > 49 1 0 0 0<br>
> > > > 50 1 0 0 0<br>
> > > ><br>
> > > > Quoting Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>:<br>
> > > ><br>
> > > > > <a href="mailto:gadies@fh.huji.ac.il">gadies@fh.huji.ac.il</a> wrote:<br>
> > > > ><br>
> > > > > Please generate replies to the mailing list sensibly. It's very hard<br>
> > > > to<br>
> > > > > work out who you are quoting where in this email. It'd be easy just<br>
> > > > to<br>
> > > > > ignore it, and that's the last thing you should want.<br>
> > > > ><br>
> > > > >> Hello,<br>
> > > > >><br>
> > > > >> I'm trying to run a simulation with one lipid molecule in a fixed<br>
> > > > >> simulation box without pbc.<br>
> > > > >> I set position restraints on one of the atoms and I seem to keep on<br>
> > > > >> getting the following error:<br>
> > > > ><br>
> > > > > Why do you want MD of a single lipid and a position restraint on one<br>
> > > > > atom? If you just want to see a lipid wiggle around, then don't<br>
> > > > create<br>
> > > > > more numerical complexity.<br>
> > > > ><br>
> > > > >> The lipid is DPPC.The .itp file I got from a coworker that used it<br>
> > > > >> before for membrane MD simulations.<br>
> > > > >> To minimize the system I used steepest descent with the following<br>
> > > > >> parameters:<br>
> > > > ><br>
> > > > > Well if your grompp and mdrun completed successfully and without<br>
> > > > > warnings then you've probably got an OK topology and structure.<br>
> > > > ><br>
> > > > > The combination of all bond constraints, a single lipid in vacuo,<br>
> > > > > temperature coupling and a single position restraint sounds like a<br>
> > > > > recipe for a numerical disaster, i.e. blowing up. Try with fewer of<br>
> > > > > those things applied, or get a more physically-reasonable system,<br>
> > > > like<br>
> > > > > a whole membrane.<br>
> > > > ><br>
> > > > > Mark<br>
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> > ><br>
> > ><br>
> > > ========================================<br>
> > ><br>
> > > Justin A. Lemkul<br>
> > > Graduate Research Assistant<br>
> > > Department of Biochemistry<br>
> > > Virginia Tech<br>
> > > Blacksburg, VA<br>
> > > <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br>
> > > <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br>
> > ><br>
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><br>
<br>
<br>
<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br>
<br>
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</blockquote></div><br>