[gmx-users] Reducing Standard Error output

Jack Shultz js at drugdiscoveryathome.com
Sun Dec 6 19:22:27 CET 2009

>> 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
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

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