[gmx-users] links warnangles
vferrario at units.it
vferrario at units.it
Wed Feb 2 14:33:14 CET 2011
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...
Valerio
"Justin A. Lemkul" <jalemkul at vt.edu> ha scritto:
>
>
> vferrario at units.it wrote:
>> Dear all,
>> I'm dealing with a simulation of a polymer in CHCL3, the polymer
>> works good, but I have some problems with the CHCL3 definition in
>> GROMOS 53a6 ff.
>> I've taken the CHCL3 definition from the automated topology builder website:
>>
>> http://compbio.biosci.uq.edu.au/atb/download.py?molid=1597&file=itp_uniatom
>>
>> So the itp file of my CHCL3 definition is:
>>
>> [ moleculetype ]
>> ; Name nrexcl
>> CLF 3
>>
>> [ atoms ]
>> ; nr type resnr residue atom cgnr charge mass
>> typeB chargeB massB
>> 1 CCL 1 CLF CCl 1 0.179 12.011
>> ; qtot 0.179
>> 2 HCL 1 CLF HCl 1 0.082 1.008
>> ; qtot 0.261
>> 3 CLCL 1 CLF CL1 1 -0.087 35.453
>> ; qtot 0.174
>> 4 CLCL 1 CLF CL2 1 -0.087 35.453
>> ; qtot 0.087
>> 5 CLCL 1 CLF CL3 1 -0.087 35.453
>> ; qtot 0
>>
>> [ constraints ]
>> 1 3 1 0.1758
>> 1 4 1 0.1758
>> 1 5 1 0.1758
>> 2 3 1 0.233839
>> 2 4 1 0.233839
>> 2 5 1 0.233839
>> 3 4 1 0.290283
>> 3 5 1 0.290283
>> 4 5 1 0.290283
>>
>> I've generated a box of solvent, but when I try to minimize it with
>> the following mdp file:
>>
>> title = Minimization
>> cpp = /lib/cpp
>> include = -I../top
>> constraints = none
>> integrator = steep
>> emtol = 2.5
>> emstep = 0.01
>> nsteps = 100000
>> nbfgscorr = 10
>> nstenergy = 100
>> nstxtcout = 0
>> xtc_grps = system
>> energygrps = system
>> nstlist = 5
>
> For EM, nstlist should be 1.
>
>> ns_type = grid
>> pbc = xyz
>> rlist = 1.0
>> coulombtype = cut-off
>
> Plain cutoffs lead to bad artifacts and thus should generally not be used.
>
>> 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
>>
>> The system crash giving me the following error:
>>
>> Fatal error:
>> Too many LINCS warnings (1413)
>> If you know what you are doing you can adjust the lincs warning
>> threshold in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>>
>> My question is: why the system crash and why LINCS warnings are
>> generated if all the molecule is constrained? What shell I do to
>> avoid these probles? New CHCL3 definition?
>
> The charges and atom types match exactly what the force field
> prescribes, so those are probably solid.
>
> You need to simplify the problem. You built a box, but it is
> failing. Does an EM of a single molecule work, or does it fail as
> well? Consult the following:
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>
> -Justin
>
>> Please help me, thank you in advance.
>>
>> Valerio
>>
>>
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>>
>>
>
> --
> ========================================
>
> 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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