[gmx-users] links warnangles
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 2 15:12:44 CET 2011
vferrario at units.it wrote:
> Seems that the new definition I've found works, but it is still unclear
> to me why...
>
There was a post long ago that I seem to remember reported the same problem.
Since there is no true bond between H and C, the H position is basically
triangulated by all of the other atoms. There should not be a bond between H
and C, since it should be constrained, yielding too many degrees of freedom.
Seems to me that these rigid Gromos96 solvent models are a little strange.
-Justin
> 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.
>
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list