[gmx-users] links warnangles

[vferrario at units.it]

Seems that the new definition I've found works, but it is still  
unclear to me why...

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
>>
>> ========================================
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at  
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www  
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at  
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww  
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



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