Dear Michael: I have uploaded them as http://redmine.gromacs.org/issues/1306
It does not crash immediately. The crash is stochastic, giving a segfault between 200 and 5000 integration steps. That made me think it was a simple exploding system problem, but there are other things (listed in my original post) that make me think otherwise. Most notably, the drug is fine in both water and vacuum. I have also built numerous systems and get the crash in each one. My actual production system also has a protein, but during debugging I found that the error persists in a simple and small water solution. Thank you for your assistance. Chris. -- original message -- Chris, can you post a redmine on this so I can look at the files? Also, does it crash immediately, or after a while? On Thu, Jul 18, 2013 at 2:45 PM, Christopher Neale <chris.neale at mail.utoronto.ca> wrote: > Dear Users: > > I have a system with water and a drug (54 total atoms; 27 heavy atoms). The > system is stable when I simulate it for 1 ns. However, Once I add the > following options to the .mdp file, the run dies after a few ps with a > segfault. > > free-energy = yes > init-lambda = 1 > couple-lambda0 = vdw-q > couple-lambda1 = none > couple-intramol = no > couple-moltype = drug > > I do not get any step files or any lincs warnings. If I look at the .xtc and > .edr files, there is no indication of something blowing up before the > segfault. I have also verified that the drug runs without any problem in > vacuum. I get the same behaviour if I remove constraints and use a timestep > of 0.5 fs. The segfault is reproducible with v4.6.1 and v4.6.3. I am using > the charmm FF, but I converted all UB angles in my drug to type-1 angles and > still got the segfault. I also get the segfault with particle decomposition > and/or while running a single thread. I am currently using the SD integrator, > but I get the same segfault with md and md-vv. Couple-intramol=yes doesn't > resolve it, neither does using separate T-coupling groups for the water and > drug. Neither does turning off pressure coupling. > > Here is the .mdp file that works fine, but gives me a segfault when I add the > free energy stuff (above): > > constraints = all-bonds > lincs-iter = 1 > lincs-order = 6 > constraint_algorithm = lincs > integrator = sd > dt = 0.002 > tinit = 0 > nsteps = 100000 > nstcomm = 1 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstxtcout = 500 > nstenergy = 500 > nstlist = 10 > nstlog=0 ; reduce log file size > ns_type = grid > vdwtype = cut-off > rlist = 0.8 > rvdw = 0.8 > rcoulomb = 0.8 > coulombtype = cut-off > tc_grps = System > tau_t = 1.0 > ld_seed = -1 > ref_t = 310 > gen_temp = 310 > gen_vel = yes > unconstrained_start = no > gen_seed = -1 > Pcoupl = berendsen > pcoupltype = isotropic > tau_p = 4 > compressibility = 4.5e-5 > ref_p = 1.0 > > I do realize that some of these settings are not ideal for a production run. > I started with the real Charmm cutoffs + PME, etc, (which also gives the > segfault) but this is what I am using right now for quick testing. > > The only thing keeping me from filing a redmine issue is that if I remove my > drug and do the FEP on one of the water molecules (using the FEP code listed > above), I have no segfault. Therefore it is clearly related to the drug, > whose parameters I built so I may have caused the problem somehow. > Nevertheless, the drug runs fine in water and in vacuum without the FEP code, > so I can't imagine what could be causing this segfault (also, the fact that > it's a segfault means that I don;t get any useful info from mdrun as to what > might be going wrong). > > Thank you, > Chris. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
