[gmx-users] links warnangles

[Justin A. Lemkul]

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

-- 
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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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