[gmx-users] links warnangles
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 2 15:32:37 CET 2011
vferrario at units.it wrote:
> No, is not working also in this case... probably the problem is with my
> mdp files:
>
I would argue that it's the coordinates that are the problem. For instance,
compare the distances expected by the topology:
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
with the actual distances found in the coordinate file:
1 3 1 0.177
1 4 1 0.177
1 5 1 0.174
2 3 1 0.240
2 4 1 0.235
2 5 1 0.235
3 4 1 0.282
3 5 1 0.290
4 5 1 0.289
The model requires 9 constraints to be satisfied in harmony. If the starting
geometry isn't perfect (or very close to it), there's probably too much
rearranging required to make the model work. Removal of the explicit H probably
yielded a set of constraints that could be somewhat satisfied by EM, but fall
apart in MD, which could be for a variety of reasons.
-Justin
> for minimization is:
>
> title = Minimization
> cpp = /lib/cpp
> include = -I../top
> constraints = none
> integrator = steep
> emtol = 5.0
> emstep = 0.01
> nsteps = 100000
> nbfgscorr = 10
> nstenergy = 100
> nstxtcout = 0
> xtc_grps = system
> energygrps = system
> nstlist = 5
> ns_type = grid
> pbc = xyz
> rlist = 1.0
> coulombtype = PME
> 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
>
> and for dynamic:
>
> title = dinamica
> ;Preprocessor
> cpp = /lib/cpp
> ;Directories to include in the topology format
> include = -I../top
> ;Run control: A leap-frog algorithm for integrating Newton's equations.
> integrator = md
> :time step in femtoseconds
> dt = 0.002
> ;number of steps
> nsteps = 500000
> ;frequency to write coordinates to output trajectory file
> nstxout = 100
> ;frequency to write velocities to output trajectory file
> nstvout = 100
> ;frequency to write energies to log file
> nstlog = 100
> ;frequency to write energies to energy file
> nstenergy = 100
> ;frequency to write coordinates to xtc trajectory
> nstxtcout = 100
> ;group(s) to write to xtc trajectory
> xtc_grps = system
> ;group(s) to write to energy file
> energygrps = system
> ;Frequency to update the neighbor list (and the long-range forces,
> ;when using twin-range cut-off's).
> nstlist = 100
> ;Make a grid in the box and only check atoms in neighboring grid cells
> ;when constructing a new neighbor list every nstlist steps.
> ns_type = grid
> ;cut-off distance for the short-range neighbor list
> rlist = 1.4
> ;treatment of electrostatic interactions
> coulombtype = cut-off
> rcoulomb = 1.4
> ;treatment of van der waals interactions
> rvdw = 1.4
> ; Periodic boudary conditions in all the directions
> pbc = xyz
> ;Temperature coupling
> tcoupl = berendsen
> tc-grps = system
> tau_t = 0.1
> ref_t = 300
> ;Pressure coupling
> Pcoupl = berendsen
> Pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 3e-5
> ref_p = 100
> ;Velocity generation
> gen_vel = yes
> gen_temp = 300
> gen_seed = 176458
>
> Any ideas? Thanks a lot.
>
> 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
>>>
>>> ========================================
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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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