[gmx-users] pressure scaling more than 1%
nanyu101
nanyu101 at sina.com
Wed Feb 19 06:50:37 CET 2003
Dear gmx-users,
I have try to make a hole for my ion channel.
grompp -f run.mdp -o insert.tpr -c dppc.pdb -r dppc.pdb -p dppc.top
mdrun -v -hole -holep hp.mdp -deffnm insert
But the system told as follows.And I will show you my run.mdp later.
Step 631 Warning: pressure scaling more than 1%, mu: 1.04684 1.04684 1.04684
Step 632 Warning: pressure scaling more than 1%, mu: 104.213 104.213 104.213
Step 633 Warning: pressure scaling more than 1%, mu: 2.66535e+07 2.66535e+07 2.66535e+07
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
Pressure Coupling:
title = Yo
cpp = /lib/cpp
define = -DPOSRES
constraints = none
integrator = md
dt = 0.001 ; ps !
nsteps = 5000 ; total 10 ps.
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.8
rcoulomb = 1.4
rvdw = 0.8
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = DPP SOL
tau_t = 0.1 0.1
ref_t = 300 300
; Energy monitoring
energygrps = DPP SOL
; Pressure coupling is not on
Pcoupl = berendsen
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = no
Would anyone give me any suggestions?Thanks very much.
Best wishes,
Xianhui Wu
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