[gmx-users] links warnangles
vferrario at units.it
vferrario at units.it
Wed Feb 2 15:22:11 CET 2011
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
vferrario at 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" <jalemkul at vt.edu> ha scritto:
>
>>
>>
>> Justin A. Lemkul wrote:
>>>
>>>
>>> vferrario at 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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