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<div class="gmail_quote">On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>></span> wrote:<br>
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<div class="h5">On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>></span> wrote:<br>
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<div>On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
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<div><br><br>Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Dear Gmx Users,<br> I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp:<br>
<br>integrator = md ; leap-frog integrator<br><br>nsteps = 1000000 ; 0.0005 * 1000000 = 0.5 ns<br><br>dt = 0.0005 ; 0.5 fs<br><br>; Output control<br><br>nstxout = 10000<br><br>nstxtcout = 10000 ; xtc compressed trajectory output every 2 ps<br>
<br>nstenergy = 10000 ; save energies every 2 ps<br><br>nstlog = 10000 ; update log file every 2 ps<br><br>; Bond parameters<br><br>continuation = no<br><br>constraints = none<br><br>; Neighborsearching<br><br>ns_type = simple ; search neighboring grid cells<br>
<br>nstlist = 0 ; 10 fs<br><br>rlist = 0 ; short-range neighborlist cutoff (in nm)<br><br>; Infinite box with no cutoffs<br><br>pbc = no<br><br>rcoulomb = 0 ; short-range electrostatic cutoff (in nm)<br><br>coulombtype = cut-off<br>
<br>vdwtype = cut-off<br><br>rvdw = 0 ; short-range van der Waals cutoff (in nm)<br><br>epsilon_rf = 0<br><br>comm_mode = angular ; remove angular and com motions<br><br>; implicit solvent<br><br>implicit_solvent = GBSA<br>
<br>gb_algorithm = OBC<br><br>gb_epsilon_solvent = 80.0<br><br>sa_surface_tension = 2.25936<br><br>rgbradii = 0<br><br>sa_algorithm = Ace-approximation<br><br>nstgbradii = 1<br><br>; Temperature coupling is on<br><br>Tcoupl = v-rescale<br>
<br>tau_t = 0.1<br><br>tc_grps = system<br><br>ref_t = 298<br><br>; Velocity generation<br><br>gen_vel = yes ; Velocity generation is on<br><br>gen_temp = 298.0<br><br>gen_seed = -1<br><br>Then after grompp I am trying to run the simulation on the cluster:<br>
<br>mdrun -pd -deffnm nvt500ps<br><br>My log file:<br><br>Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1#<br><br>Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision)<br><br>Starting 8 threads<br><br>Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1#<br>
<br>Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1#<br><br>Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1#<br><br>starting mdrun 'Protein'<br><br>1000000 steps, 500.0 ps.<br><br>Segmentation fault<br>
<br> <br>Do you have any clue what is happening?<br><br></blockquote><br></div></div>Try running in serial or with a maximum of 2 threads. Your problem could be related to <a href="http://redmine.gromacs.org/issues/777" target="_blank">http://redmine.gromacs.org/<u></u>issues/777</a>. You will need to upgrade to 4.5.5 (serial should work on 4.5.4).<br>
<br>-Justin<br><br></blockquote>
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<div>Thank you. What do you mean by running in serial? Well... with 2 threads it does not make sense to use implicit solvent. Will 4.5.5 resolve this problem?</div><span><font color="#888888">
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<div>Indeed, it works in serial. Will version 4.5.5 resolve it run it on e.g. 12 nodes?</div><span class="HOEnZb"><font color="#888888">
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<div>Sorry, the same problem :</div>
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<div><span lang="EN">
<p>Initial temperature: 298.398 K</p>
<p>Started mdrun on node 0 Thu Mar 1 15:56:04 2012</p>
<p>Step Time Lambda</p>
<p>0 0.00000 0.00000</p>
<p>Energies (kJ/mol)</p>
<p>Bond U-B Proper Dih. Improper Dih. CMAP Dih.</p>
<p>2.27391e+02 4.27461e+02 1.27733e+03 2.73432e+01 -6.95645e+02</p>
<p>GB Polarization Nonpolar Sol. LJ-14 Coulomb-14 LJ (SR)</p>
<p>inf 3.59121e+02 6.85627e+02 3.68572e+04 -7.57140e+02</p>
<p>Coulomb (SR) Potential Kinetic En. Total Energy Conserved En.</p>
<p>-3.30643e+04 inf nan nan nan</p>
<p>Temperature Pressure (bar)</p>
<p>nan 0.00000e+00</p></span></div>
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<div class="gmail_quote"><span class="HOEnZb"><font color="#888888"><br></font></span>- <br>==============================<u></u>==========<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>
Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br><br>==============================<u></u>==========<span><font color="#888888"><br>
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