Hi,<br><br>Sorry for the incomplete details. Here they are now:<br><br>I started with a well-equilibrated POPC bilayer, and changed one POPC lipid to a lipid of my interest. I wrote the topology file for the new lipid accordingly. <br>
<br>After that, I did some simple steepest descent minimization, and followed it up by dynamics. Here is the .mdp file for the runs. There is a preceding 25,000-step simulation where the initial velocities are assigned. The mdp file below is what is being used for equilibrium dynamics.<br>
<br>thank you for the suggestions. I will also explore the archives<br><br>;<br>; Input file<br>;<br>;-------------------------<br>; BASICS<br>;-------------------------<br>title = dummy-file<br>cpp = /usr/bin/cpp<br>
integrator = md<br>tinit = 0<br>init_step = 25000<br>nsteps = 100000<br>dt = 0.002<br>;-------------------------<br>; BOND PARAMETERS<br>;-------------------------<br>
constraints = hbonds<br>constraint_algorithm = lincs<br>unconstrained_start = yes<br>lincs_order = 4<br>lincs_warnangle = 30<br>;-------------------------<br>; OUTPUT CONTROL<br>;-------------------------<br>
nstxout = 5000 ; positions<br>nstvout = 5000 ; velocity<br>nstlog = 5000 ; energies to log file<br>nstenergy = 5000 ; energy to energy file<br>;-------------------------<br>
; MISCELLANEOUS<br>;-------------------------<br>comm_mode = linear<br>nstlist = 10<br>ns_type = grid<br>pbc = xyz<br>; ------------------<br>; NONBONDED INTERACTIONS<br>
; ------------------<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rlist = 1.0<br>rvdw = 1.0<br>fourierspacing = 0.1<br>pme_order = 4<br>
ewald_rtol = 1e-5<br>; ---------------------------<br>; NPT<br>; ---------------------------<br>Tcoupl = berendsen<br>tc-grps = LIP Solvent<br>tau_t = 0.1 0.1<br>
ref_t = 313.0 313.0<br>Pcoupl = berendsen<br>Pcoupltype = semiisotropic<br>tau_p = 1.0 1.0<br>compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0<br>
; ---------------------------<br>gen_vel = no<br>; ---------------------------<br><br><br><br><br><br><br><div class="gmail_quote">On Fri, Apr 4, 2008 at 6:44 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;"><div class="Ih2E3d">Quoting "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>:<br>
<br>
> Quoting maria goranovic <<a href="mailto:mariagoranovic@gmail.com">mariagoranovic@gmail.com</a>>:<br>
><br>
> > Dear All<br>
> ><br>
> > I am running a 128-lipid bilayer simulation with standard parameters. The<br>
> > simulation abruptly crashed after 2 ns, and a look into the pdb files<br>
> > suggested that bonds were being broken and eventually the lipids explode. I<br>
> > tried increasing the cutoffs from 1.0 to 1.4, and this time also, the<br>
> > simulation exploded, but at a different time point.<br>
<br>
</div>And as an aside, broken bonds are only a visualization effect; mdrun doesn't<br>
write broken molecules. Also, providing your .mdp file would be of use.<br>
<font color="#888888"><br>
-Justin<br>
</font><div><div></div><div class="Wj3C7c"><br>
> ><br>
> > The energy remains nice and stable till the explosion.<br>
> ><br>
> > How does one fix this ? What is planting these bombs ?<br>
><br>
> You'll have to describe how you minimized and equilibrated your bilayer<br>
> before<br>
> we'll have any idea what's going on. Also have a thorough look through the<br>
> archives; many users have posted about bilayers exploding (including yours<br>
> truly).<br>
><br>
> -Justin<br>
><br>
> ><br>
> > Thank you for suggestions.<br>
> ><br>
> > --<br>
> > Maria G.<br>
> > Technical University of Denmark<br>
> > Copenhagen<br>
> ><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>
> ========================================<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>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen