[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
>>>
>>>
>>> ----------------------------------------------------------------
>>> This message was sent using IMP, the Internet Messaging Program.
>>>
>>>
>>
>> -- 
>> ========================================
>>
>> 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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> 
> 
> 
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> 
> 
> 

-- 
========================================

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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