[gmx-users] Peptide interactions with membrane lipids
Aswin Sai Narain
aswin_biogenie at yahoo.co.uk
Sun Oct 12 05:55:02 CEST 2003
Hi all
I have a major doubt. How do I actually go about placing the peptide in the
membrane environment? Is it correct to use genbox using dppc as solvent?
Because, when I did this, the following happened.
I tried running the em. I used the following mdp file:
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
cpp = /lib/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 10000
;
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.8
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
The em simulation showed the following:
Steepest Descents:
Tolerance = 2.00000e+03
Number of steps = 10000
Warning: 1-4 interaction at distance larger than 1
These are ignored for the rest of the simulation
turn on -debug for more information
Step= 1, Dmax= 1.0e-02 nm, Epot= 2.94805e+09 Fmax= 1.01461e+09, atom=
7856
Step= 2, Dmax= 1.2e-02 nm, Epot= 2.68462e+09 Fmax= 1.79138e+08, atom=
7406
Step= 3, Dmax= 1.4e-02 nm, Epot= 2.62547e+09 Fmax= 5.29382e+07, atom=
8436
Step= 4, Dmax= 1.7e-02 nm, Epot= 2.61144e+09 Fmax= 4.96408e+07, atom=
8006
Step= 5, Dmax= 2.1e-02 nm, Epot= 2.60584e+09 Fmax= 2.32306e+07, atom=
8585
Step= 6, Dmax= 2.5e-02 nm, Epot= 2.59659e+09 Fmax= 1.70494e+07, atom=
8006
Step= 7, Dmax= 3.0e-02 nm, Epot= 2.58519e+09 Fmax= 4.06876e+06, atom=
8007
Step= 8, Dmax= 3.6e-02 nm, Epot= 2.53756e+09 Fmax= 9.73282e+07, atom=
8088
Step= 9, Dmax= 4.3e-02 nm, Epot= 2.53431e+09 Fmax= 5.31674e+06, atom=
8088
Step= 10, Dmax= 5.2e-02 nm, Epot= 2.48471e+09 Fmax= 2.74124e+06, atom=
2182
Step= 11, Dmax= 6.2e-02 nm, Epot= 2.37340e+09 Fmax= 2.67713e+06, atom=
2182
Step= 12, Dmax= 7.4e-02 nm, Epot= 2.24401e+09 Fmax= 2.60029e+06, atom=
2182
Step= 13, Dmax= 8.9e-02 nm, Epot= 2.09428e+09 Fmax= 3.99132e+06, atom=
8307
Step= 14, Dmax= 1.1e-01 nm, Epot= 1.98544e+09 Fmax= 3.43059e+07, atom=
8307
Step= 15, Dmax= 1.3e-01 nm, Epot= 1.97118e+09 Fmax= 6.31594e+07, atom=
8306
Step= 16, Dmax= 1.5e-01 nm, Epot= 1.96094e+09 Fmax= 2.42373e+06, atom=
2182
Step= 17, Dmax= 1.8e-01 nm, Epot= 1.68085e+09 Fmax= 2.32879e+07, atom=
2269
Step= 19, Dmax= 1.1e-01 nm, Epot= 1.66439e+09 Fmax= 3.53242e+07, atom=
8006
Step= 20, Dmax= 1.3e-01 nm, Epot= 1.65200e+09 Fmax= 1.20352e+07, atom=
8006
Step= 21, Dmax= 1.6e-01 nm, Epot= 1.60965e+09 Fmax= 3.01545e+06, atom=
8006
Step= 25, Dmax= 2.4e-02 nm, Epot= 1.58496e+09 Fmax= 2.16532e+06, atom=
2182
Step= 28, Dmax= 7.2e-03 nm, Epot= 1.57481e+09 Fmax= 2.15790e+06, atom=
2182
Step= 30, Dmax= 4.3e-03 nm, Epot= 1.56873e+09 Fmax= 2.15345e+06, atom=
2182
Step= 34, Dmax= 6.5e-04 nm, Epot= 1.56782e+09 Fmax= 2.15278e+06, atom=
2182
Step= 38, Dmax= 9.7e-05 nm, Epot= 1.56768e+09 Fmax= 2.15268e+06, atom=
2182
Step= 45, Dmax= 1.8e-06 nm, Epot= 1.56768e+09 Fmax= 2.15268e+06, atom=
2182
Step= 46, Dmax= 2.2e-06 nm, Epot= 1.56767e+09 Fmax= 2.15267e+06, atom=
2182
Step= 48, Dmax= 1.3e-06 nm, Epot= 1.56376e+10 Fmax= 3.15365e+12, atom=
8530
Stepsize too small (6.55034e-07 nm)Converged to machine precision,
but not to the requested precision (2000)
writing lowest energy coordinates.
Back Off! I just backed up amem.trr to ./#amem.trr.1#
Back Off! I just backed up amem.gro to ./#amem.gro.1#
Steepest Descents did not converge in 49 steps
Potential Energy = 1.56767e+09
Maximum force: 2.15267e+06
gcq#1: "I Live the Life They Wish They Did" (Tricky)
For the md i used this mdp:
title = Yo
cpp = /lib/cpp
constraints = all-bonds
constraint_algorithm= Shake
integrator = md
dt = 0.002
nsteps = 5000
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.8
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein SOL DPPC
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Energy monitoring
energygrps = Protein SOL DPPC
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 300 K.
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
And the errors were:
Warning: 1-4 interaction at distance larger than 1
These are ignored for the rest of the simulation
turn on -debug for more information
Wrote pdb files with previous and current coordinates
step 0
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.
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]
Plz help me out.
Aswin Sai Narain. S
Student
Centre for Biotechnology
Anna University
Chennai 25
The woods are lovely, dark and deep
I have promises to keep
And miles to go before I sleep
And miles to go before I sleep
- Robert Frost
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