No, is not working also in this case... probably the problem is with
my mdp files:
for minimization is:
title = Minimization
cpp = /lib/cpp
include = -I../top
constraints = none
integrator = steep
emtol = 5.0
emstep = 0.01
nsteps = 100000
nbfgscorr = 10
nstenergy = 100
nstxtcout = 0
xtc_grps = system
energygrps = system
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.15
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
optimize_fft = yes
tcoupl = no
pcoupl = no
gen_vel = no
constraint_algorithm = LINCS
lincs_order = 8
lincs_iter = 2
nstlog = 100
lincs_warnangle = 90
and for dynamic:
title = dinamica
;Preprocessor
cpp = /lib/cpp
;Directories to include in the topology format
include = -I../top
;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator = md
:time step in femtoseconds
dt = 0.002
;number of steps
nsteps = 500000
;frequency to write coordinates to output trajectory file
nstxout = 100
;frequency to write velocities to output trajectory file
nstvout = 100
;frequency to write energies to log file
nstlog = 100
;frequency to write energies to energy file
nstenergy = 100
;frequency to write coordinates to xtc trajectory
nstxtcout = 100
;group(s) to write to xtc trajectory
xtc_grps = system
;group(s) to write to energy file
energygrps = system
;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist = 100
;Make a grid in the box and only check atoms in neighboring grid cells
;when constructing a new neighbor list every nstlist steps.
ns_type = grid
;cut-off distance for the short-range neighbor list
rlist = 1.4
;treatment of electrostatic interactions
coulombtype = cut-off
rcoulomb = 1.4
;treatment of van der waals interactions
rvdw = 1.4
; Periodic boudary conditions in all the directions
pbc = xyz
;Temperature coupling
tcoupl = berendsen
tc-grps = system
tau_t = 0.1
ref_t = 300
;Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 3e-5
ref_p = 100
;Velocity generation
gen_vel = yes
gen_temp = 300
gen_seed = 176458
Any ideas? Thanks a lot.
Valerio
vferra...@units.it ha scritto:
The molecule is rigid because it's all constrained and the
coordinates of the single molecule seem to be ok:
CLF
5
1CLF CCl 1 3.041 1.571 0.924
1CLF HCl 2 3.001 1.637 0.845
1CLF CL1 3 3.071 1.661 1.073
1CLF CL2 4 3.186 1.493 0.867
1CLF CL3 5 2.916 1.452 0.963
0.50000 0.50000 0.50000
I've found another CHCL3 model on the GROMACS website by user
contribution, but the difinition is closed to mine, exept for the
hydrogen atom which is not considered as an independent particle but
is considered with the carbon:
[ atomtypes ]
;type mass charge ptype sigma epsilon
CH 12.01100 0.420 A 3.80000e-01 3.26944e-01
CLCL3 35.45300 -0.140 A 3.47000e-01 1.25604e+00
[ moleculetype ]
; name nrexcl
CCl3 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 CH 1 CCl4 CT1 1 0.420
2 CLCL3 1 CCl4 Cl2 1 -0.140
3 CLCL3 1 CCl4 Cl3 1 -0.140
4 CLCL3 1 CCl4 Cl4 1 -0.140
[ constraints ]
; ai aj funct b0
1 2 1 0.17580
1 3 1 0.17580
1 4 1 0.17580
2 3 1 0.2902831
2 4 1 0.2902831
3 4 1 0.2902831
Probably is the definition of that single hydrogen that cause
problems, I'll check this new definition.
Valerio
"Justin A. Lemkul" <jalem...@vt.edu> ha scritto:
Justin A. Lemkul wrote:
vferra...@units.it wrote:
I've just tried with a single CHCL3 molecule, here's the output:
Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money
NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2 x 1 x 1
Step -1, time -0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 301.323604, max 324.810791 (between atoms 1 and 3)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Back Off! I just backed up step-1b_n1.pdb to ./#step-1b_n1.pdb.2#
Back Off! I just backed up step-1c_n1.pdb to ./#step-1c_n1.pdb.2#
Wrote pdb files with previous and current coordinates
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
Steepest Descents:
Tolerance (Fmax) = 2.50000e+00
Number of steps = 100000
Step= 0, Dmax= 1.0e-02 nm, Epot= 0.00000e+00 Fmax=
0.00000e+00, atom= 0
writing lowest energy coordinates.
Back Off! I just backed up clfmin.gro to ./#clfmin.gro.1#
Steepest Descents converged to Fmax < 2.5 in 1 steps
Potential Energy = 0.0000000e+00
Maximum force = 0.0000000e+00 on atom 0
Norm of force = 0.0000000e+00
NOTE: 7 % of the run time was spent communicating energies,
you might want to use the -nosum option of mdrun
gcq#320: "Do You Have Sex Maniacs or Schizophrenics or
Astrophysicists in Your Family?" (Gogol Bordello)
The minimum is reached without steps, so... I don't know if the
single atom minimization wors or not...
It certainly didn't work. At the outset of the process, you
instantly got a LINCS warning, indicating instability. This would
indicate to me that the model itself is unstable. I'm sorry to
say I don't know what to suggest, as the Gromos96 chloroform model
should be rigid, and your topology reproduces what is in the force
field .rtp entry for chloroform.
I guess I'm blaming this all on the topology, but it could also be
that your coordinates are messed up and they can't be resolved by
EM. Check into that, as well.
-Justin
--
========================================
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
========================================
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