[gmx-users] LINCS warning in md run

[Justin Lemkul]

On 9/18/12 7:22 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> I need the rest of the structure just as it is now because I want to do
> electrostatic analysis with it.
> I just added the phosphate manually and so I want to minimize and run a
> short MD with it.
>
> I added the dihedraltype of the amber database
> (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
> to the ffbonded file.
> And additionally I looked at the protein and made all the residues which
> could somehow influence the protein flexible so that eventual clashes can
> be repaired.
> But still I got the error:
>
> ..Step 3612, time 3.612 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000008, max 0.000031 (between atoms 975 and 978)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      976    979   32.6    0.0961   0.0960      0.0960
>
> Step 3613, time 3.613 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000237, max 0.001400 (between atoms 976 and 979)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      976    979   33.4    0.0960   0.0959      0.0960
> ..
>

So what are these atoms?  This gives you a hint at the origin of the problem. 
Have you followed the troubleshooting advice at 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System? 
  It covers basically everything anyone would suggest to you for these types of 
errors.

Posting an .mdp file would be useful in case you're doing something wrong with 
respect to the run parameters.

> Too many LINCS warnings (1000)
>
>
> I already minimized the protein and everything was fine. There were no
> errors:
>

These are results are not "fine" at all.  The maximum force on atom 979 is huge, 
and that's what's causing things to spin out of control very early in the MD.

-Justin

> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -7.7436938e+05
> Maximum force     =  8.6871973e+03 on atom 979
> Norm of force     =  7.1224258e+01
>
> gcq#49: "You Could Make More Money As a Butcher" (F. Zappa)
>
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -7.7436938e+05
> Maximum force     =  8.6871973e+03 on atom 979
> Norm of force     =  7.1224258e+01
>
>
> And also during the grompp run there are no errors.
> Can you please help me to find out where the problem lies?
>
>
> Thank you,
>   Eva
>
>
>>
>>
>> On 9/13/12 5:50 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>> Ah okey. Thank you.
>>> I will write them.
>>>
>>> Hmm, but the protein is a crystal structure from pdb with a resolution
>>> of
>>> 1.2. I already added the hydrogen atoms to this structure and there I
>>> already minimized them and made a md run. And there were no errors. And
>>> now I only added the phosphate to the minimized structure. So I thought
>>> that I only had to minimize the phosphate and the residue it bound on.
>>> Or is there a mistake in my thought here?
>>
>> If adding the phosphate resulted in a crash, then clearly that's the
>> problem.  I
>> don't understand why you would run EM on just the phosphate and keep the
>> rest of
>> the protein structure frozen.  Again, that potentially prevents clashes
>> from
>> being resolved.  I don't understand what value there is in only minimizing
>> the
>> phosphate.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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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>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================