On 8/21/12 12:59 PM, virginia miguel wrote:
Hi everyone; I am running a MD simulation of a 40 kDa protein bound to ADP in
GROMACS VERSION 4.5.5. I made three minimization with restrains in protein,
backbone and c-alpha, in that order, and two equilibration with 150 and 300K
using backbone restrains. But when I run my md I get this error
(...)
Step 234604:
The charge group starting at atom 3430 moved than the distance allowed by the
domain decomposition (3.219980) in direction X
distance out of cell -65.799425
Old coordinates: 4.304 3.918 3.886
New coordinates: -62.579 4.743 6.132
Old cell boundaries in direction X: 3.220 6.439
New cell boundaries in direction X: 3.220
6.440
-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 4124
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
-------------------------------------------------------
(..)
The atom corresponds to the ADP
the mdp file I am using is the following and I am running it with
mdrun -nt 4 -npme 1 -v -s topol.tpr -o traj.trr -x traj.xtc -c din.pdb -e
ener.edr -g md.log
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
title = Yo
define =
integrator = md
dt = 0.005
nsteps = 40000000
nstxout = 20000
nstvout = 20000
nstfout = 0
nstxtcout = 500
nstlog = 1000
nstenergy = 500
nstlist
= 4
ns_type = grid
energygrps = Protein SOL
coulombtype = pme
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc-grps = !SOL SOL
tau_t = 0.1
0.1
ref_t = 300 300
; Energy monitoring
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed
= 173529
constraints = all-bonds
If any one can help me with this error I would appreciate it very much!. Thank
you in advance, Virginia.
Your timestep (5 fs) is too large. Reduce it to 2 fs and try again.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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