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
