>> >> Apparently this code is only used if the app is in verbose mode. So I >> guess we have two choices: >> 1) either find the cause of the lincs warnings > > That is always necessary if you don't want an expensive random number > generator. Your simulation system is ill conditioned, and the lincs warnings > will exist and be reported in at least the .log file regardless of the > verbosity. >
Initialy we had this minimized using these parameters define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol = 1000 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes (I borrowed it from acpypi tutorial) Apparently this does not minimize the system quite enough. So I am now reducing emtol to 10 and nsteps to 10,000. I will see if I get convergence. Are there other recomendations regarding minimization? Should we consider constraining the molecule? One idea is 1st minimization with constraints 2nd minimization without constraints 3rd md with constraints 4th md without constraints -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
