[gmx-users] Annealing--Fatal Error message can't be right.
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 9 19:35:35 CET 2011
William Welch wrote:
> Dear kind helpers,
> I am using GROMACS 4.0.5. I cannot find an answer to my exact problem
> in the archives. I am getting the error message "not enough annealing
> values 2 for 1 group" but I do not have 2 values specified for
> annealing--not for any of the variables. I tried reading the source code
> in the file specified in the error message, but I don't know what all
> the variables are. I can't figure out where it thinks I have 2 values
> specified. My annealing section follows what is given in the manual. I
> am using a simple mdp file adapted from the the tutorial files which is
> as follows:
> title = Yo
> cpp = /usr/bin/cpp
> constraints = none
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 480000 ; total 500 ps.
> nstcomm = 1
> nstxout = 50
> nstvout = 100
> nstfout = 0
> nstlog = 100
> nstenergy = 100
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.0
> pbc = xyz
> ; Annealing
> annealing = single periodic
> annealing_time = 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80
> annealing_points = 17
> annealing_temp = 300 330 360 390 420 450 480 510 480 450 420 390
> 360 330 300 300 300
> ; Isotropic pressure coupling is now on
> Pcoupl = berendsen
> Pcoupltype = isotropic
> compressibility = 4.5e-5
> ref_p = 0.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 350.0
> gen_seed = 173529
> I've tried turning on Tcoupl and specifying the system as a group, which
> requires a reference temperature and a time constant. I don't think
> annealing and coupling to a bath makes sense, but when I do it I just
> get the same error.
> Certainly it there is some simple issue?
1. You need to use some sort of thermostat, or else nothing is controlling the
2. You haven't defined any tc-grps, but you're implicitly creating two groups
(based on "annealing = single periodic"). This is where the fatal error is
coming from - 2 annealing groups, but one tc-grp (System, implicitly, since you
haven't defined any).
3. "annealing_points" is not a real keyword, but "annealing_npoints" is.
4. You're generating velocities at 350 K, but starting annealing at 300 K. This
is not an error as such, but it's probably going to affect how well you move
through the target temperatures.
There is an example of proper annealing usage in the online manual:
> Will Welch
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users