about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband. Below is a copy of my mdp file.<div><br></div><div><div>title = BMIM+PF6</div><div>cpp = /lib/cpp</div><div>constraints = all_bonds</div>
<div>integrator = md</div><div>dt = 0.004 ; ps !</div><div>nsteps = 20000000 ; total 4ns.</div><div>nstcomm = 1</div><div>nstxout = 50000</div><div>nstvout = 50000</div>
<div>nstfout = 0</div><div>nstlog = 5000</div><div>nstenergy = 5000</div><div>nstxtcout = 25000</div><div>nstlist = 10</div><div>ns_type = grid</div>
<div>pbc = xyz</div><div>coulombtype = PME</div><div>vdwtype = Shift</div><div>rlist = 1.0</div><div>rcoulomb = 1.0</div><div>rvdw = 1.0</div>
<div>fourierspacing = 0.6</div><div>;pme_order = 4</div><div>ewald_rtol = 1e-5</div><div>; Berendsen temperature coupling is on in two groups</div><div>Tcoupl = berendsen</div><div>
tc_grps = BMI PF6 </div><div>tau_t = 0.1 0.1</div><div>ref_t = 300 300</div><div>nsttcouple = 1</div><div>; Energy monitoring</div><div>energygrps = BMI PF6</div>
<div>; Isotropic pressure coupling is now on</div><div>Pcoupl = berendsen</div><div>pcoupltype = isotropic</div><div>;pc-grps = BMI PFF</div><div>tau_p = 1.0</div><div>
ref_p = 1.0</div><div>compressibility = 4.5e-5</div><div><br></div><div>; Generate velocites is off at 300 K.</div><div>gen_vel = yes</div><div>gen_temp = 300.0</div><div>gen_seed = 100000</div>
<div><br></div><br><div class="gmail_quote">On Thu, Jan 27, 2011 at 4:12 PM, Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="color:#1F497D">You will need to provide more details on the system. How many atoms, what sort of computer system is it being run on, how many nodes, copy of the mdp file etc.</span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span></p><p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Catch ya,<br><br>Dr. Dallas Warren</span></p><p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Medicinal Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;color:#1F497D">, Monash University<br>381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span></p><p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">+61 3 9903 9304<br>---------------------------------<br>When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="color:#1F497D"> </span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span></p><div style="border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt"><div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:10.0pt">From:</span></b><span style="font-size:10.0pt"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <b>On Behalf Of </b>Denny Frost<br>
<b>Sent:</b> Friday, 28 January 2011 9:34 AM<br><b>To:</b> Discussion list for GROMACS users<br><b>Subject:</b> [gmx-users] Slow Runs</span></p></div></div><div class="im"><p class="MsoNormal"> </p><p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif"">I am taking over a project for a graduate student who did MD using Gromacs 3.3.3. I now run similar simulations with Gromacs 4.5.1 and find that they run only about 1/2 to 1/3 as fast as the previous runs done in Gromacs 3.3.3. The runs have about the same number of atoms and both use opls force fields. The mdp files is virtually the same (I copied them). The only major difference is that my runs have difference species and thus have different (although smaller) itp files. The runs are stable and give reasonable thermodynamic properties - they're just slow. Has anyone had any experience with something like this? </span></p>
</div></div></div></div><br>--<br>
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