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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>I don't really know what could be the problem here.<br><br>0..180 is (confusingly) not including the end, so 180 is out of range.<br><br>The only thing I can think of (except for unknown bugs of coarse),<br>is that I corrected the coupling time of the Parrinello-Rahman barostat<br>when going from 4.0 RC4 to the official 4.0 release.<br>I guess all your old simulations were with older Gromacs releases.<br>So to get the same coupling as before, so would need to multiply tau_t by 16.6.<br>I don't know if this would help.<br><br>You did not get pressure coupling warnings before the crash?<br><br>Berk<br></div><br><br><hr id="stopSpelling">> Date: Mon, 13 Oct 2008 16:55:20 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Unexplained crashes with Gromacs-4.0<br>> <br>> <br>> Hi,<br>> <br>> I've gotten the following error with two of my simulation systems. Usually this <br>> weird "variable ci" error means the system is unstable, and I've seen it before <br>> when I've done a poor job of equilibrating. But now I'm seeing it a long time <br>> into my simulations (after 48 ns in one case, 60 ns in the other). If I simply <br>> re-submit the job, it runs fine. The error shown is as follows:<br>> <br>> -------------------------------------------------------<br>> Program mdrun_4.0_mpi, VERSION 4.0<br>> Source code file: nsgrid.c, line: 357<br>> <br>> Range checking error:<br>> Explanation: During neighborsearching, we assign each particle to a grid<br>> based on its coordinates. If your system contains collisions or parameter<br>> errors that give particles very high velocities you might end up with some<br>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>> put these on a grid, so this is usually where we detect those errors.<br>> Make sure your system is properly energy-minimized and that the potential<br>> energy seems reasonable before trying again.<br>> <br>> Variable ci has value 180. It should have been within [ 0 .. 180 ]<br>> <br>> -------------------------------------------------------<br>> <br>> It seems to me that this "ci" variable is still within the range of 0->180, if <br>> those values are inclusive.<br>> <br>> My .mdp file is as follows:<br>> <br>> title                = NPT simulation for a membrane protein<br>> ; Run parameters<br>> integrator        = md<br>> dt                = 0.002<br>> nsteps                = 5000000        10000 ps (10 ns)<br>> tinit                = 40000<br>> nstcomm                = 1<br>> ; Output parameters<br>> nstxout                = 50000                every 100 ps<br>> nstvout                = 50000<br>> nstfout                = 50000<br>> nstlog                = 5000                every 10 ps<br>> nstenergy        = 5000<br>> nstxtcout        = 5000<br>> ; Bond parameters<br>> constraint_algorithm         = lincs<br>> constraints                = all-bonds<br>> continuation                 = yes<br>> ; Cut-off's and neighborsearching<br>> nstlist                = 5<br>> ns_type                = grid<br>> rlist                = 1.2<br>> rcoulomb        = 1.2<br>> rvdw                = 1.2<br>> ; PME electrostatics parameters<br>> coulombtype        = PME<br>> fourierspacing = 0.18<br>> ;fourier_nx        = 0<br>> ;fourier_ny         = 0<br>> ;fourier_nz        = 0<br>> pme_order        = 4<br>> ewald_rtol        = 1e-5<br>> optimize_fft        = yes<br>> ; Berendsen temperature coupling is on in three groups<br>> Tcoupl                 = Nose-Hoover<br>> tc_grps                = Protein POPC SOL_NA+_CL-<br>> tau_t                = 0.1 0.1 0.1<br>> ref_t                = 310 310 310<br>> ; Pressure coupling is not on<br>> Pcoupl                = Parrinello-Rahman<br>> pcoupltype        = semiisotropic<br>> tau_p                = 2.0                <br>> compressibility        = 4.5e-5 4.5e-5<br>> ref_p                = 1.0 1.0<br>> ; Generate velocities is off<br>> gen_vel                = no<br>> gen_temp        = 310<br>> gen_seed        = 7041776<br>> ; Periodic boundary conditions are on in all directions<br>> pbc                = xyz<br>> ; Long-range dispersion correction<br>> DispCorr        = EnerPres<br>> <br>> Any ideas what's going on?<br>> <br>> Thanks,<br>> Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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