[gmx-users] links warnangles
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 2 14:39:30 CET 2011
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.
-Justin
> 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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>
>
>
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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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