While switching from NVT to NPT, i'm crashing my simulation.
The error message seen is (repeated 10 times, then mdrun aborts):
#####
Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20
-1.59647e+20 -1.59647e+20
Correcting invalid box:
old box (3x3):
old box[ 0]={-9.82630e+20, 0.00000e+00, -0.00000e+00}
old box[ 1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
old box[ 2]={ 0.00000e+00, 0.00000e+00, -1.12456e+21}
new box (3x3):
new box[ 0]={-9.82630e+20, 0.00000e+00, -0.00000e+00}
new box[ 1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
new box[ 2]={ 0.00000e+00, 8.90833e+20, -1.12456e+21}
.....
-------------------------------------------------------
Program mdrun_lam, VERSION 3.3.1
Source code file: ns.c, line: 265
Fatal error:
Box was shifted at least 10 times. Please see log-file.
-------------------------------------------------------
#####
I've searched in the archives this could be related to a non
sufficiently equilibrated system, but the first 20ps NVT run fine, so i
presume there's either a problem in the way i'm doing it (thus the
RFC-like question from the other message) or i'm missing something obvious.
Since i've tried to eliminate many errors and still get these errors
after different trials (removing shuffle and sort, generating or not
velocities while switching from pr1 to pr2, i've also tried the
"unconstrained_start=yes").
If you have any pointer, i'll be very happy to read it ...
I'm still looking at my setup system (protein in a water/spc solvent) in
order to find where is my error, but since the NVT run seems ok
(analysing precisely it at the moment, but no visual problem neither any
hint in the logs), i'm willing to understand why the switch to NPT fails.
Cheers,
Stéphane
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
title = MD simulation of OR1G1 with full explicit membrane
and solvant
; Preprocessing
cpp = /lib/cpp
define = -DPOSRE
; Run parameters
integrator = md
dt = 0.002
nsteps = 10000 ; 20 ps for PR1
nstcomm 1
comm_mode = linear
; File outuput
nstxout = 500
nstvout = 250
nstlog = 250
nstenergy = 250
nstxtcout = 500
; Molecule decomposition
xtc_grps = Protein 478 SOL CL-
energygrps = Protein 478 SOL CL-
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 0.9
; Electrostatics & VdW
coulombtype = PME
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
optimize_fft = yes ; try to get some time left for long
simulations
rcoulomb = 0.9
rvdw = 1.4
vdwtype = Cut-off
; Temperature
tcoupl = berendsen
tc-grps = Protein 478 SOL CL-
tau_t = 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300
; Pression
Pcoupl = no
Pcoupltype = isotropic
tau_p = 10
ref_p = 1.0
compressibility = 4.5e-5
; Velocities while at 300 K
gen_vel = yes
gen_temp = 300
gen_seed = -1
; Constraints
constraints = all-bonds
constraint_algorithm = lincs
freezegrps = Protein-H 478
freezedim = Y Y Y Y Y Y
title = MD simulation of OR1G1 with full explicit membrane
and solvant
; Preprocessing
cpp = /lib/cpp
define = -DPOSRE
; Run parameters
integrator = md
dt = 0.002
nsteps = 5000 ; 10 ps for PR2
nstcomm 1
comm_mode = linear
; File outuput
nstxout = 500
nstvout = 250
nstlog = 250
nstenergy = 250
nstxtcout = 500
; Molecule decomposition
xtc_grps = Protein 478 SOL CL-
energygrps = Protein 478 SOL CL-
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 0.9
; Electrostatics & VdW
coulombtype = PME
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
optimize_fft = yes ; try to get some time left for long
simulations
rcoulomb = 0.9
rvdw = 1.4
vdwtype = Cut-off
; Temperature
tcoupl = berendsen
tc-grps = Protein 478 SOL CL-
tau_t = 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300
; Pression
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 10
ref_p = 1.0
compressibility = 4.5e-5
; Velocities while at 300 K
gen_vel = no
gen_temp = 300
gen_seed = -1
; Constraints
constraints = all-bonds
constraint_algorithm = lincs
freezegrps = Protein-H
freezedim = Y Y Y
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