[gmx-users] Reducing Standard Error output

[Mark Abraham]

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