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?
Several, actually.
1. You need to use some sort of thermostat, or else nothing is controlling the
temperature.
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:
http://manual.gromacs.org/current/online/mdp_opt.html#sa
-Justin
Will Welch
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
