Jack Shultz wrote:
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
First, you need to understand that restraints and constraints are
different, and the purpose for using them. See manual for that. Also see
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
Mark
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