[gmx-users] links warnangles

[vferrario at units.it]

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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