[gmx-users] LINCS warning in md run

Tue Sep 18 14:58:41 CEST 2012

Okey,
 now I tried it without any fixed residues. But still the energy after the
minimization is not very low and I still get the LINCS warnings.

The mdp file I use for the minimization looks like this:

define                  = -DPOSRES
integrator              = steep
emtol                   = 10
nsteps                  = 1500
nstenergy               = 1
energygrps              = System
coulombtype             = PME
rcoulomb                = 0.9
rvdw                    = 0.9
rlist                   = 0.9
fourierspacing          = 0.12
pme_order               = 4
ewald_rtol              = 1e-5
pbc                     = xyz

the mdp file for the md run looks like this:

define          = -DPOSRES
integrator              = md
dt                      = 0.001
nsteps          = 5000
nstxout         = 100
nstvout         = 0
nstfout         = 0
nstlog          = 1000
nstxtcout               = 500
nstenergy               = 5
energygrps              = Protein Non-Protein
nstcalcenergy   = 5
nstlist         = 10
ns-type         = Grid
pbc                     = xyz
rlist           = 0.9
coulombtype             = PME
rcoulomb                = 0.9
rvdw            = 0.9
fourierspacing          = 0.12
pme_order               = 4
ewald_rtol              = 1e-5
gen_vel         = yes
gen_temp                = 200.0
gen_seed                = 9999
constraints             = all-bonds
tcoupl          = V-rescale
tc-grps         = Protein  Non-Protein
tau_t           = 0.1     0.1
ref_t           = 298     298
pcoupl          = no

The output of the minimization run is:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -7.9280412e+05
Maximum force     =  1.0772942e+04 on atom 979
Norm of force     =  9.6685356e+01

The output of the MD run is:

Step 1031, time 1.031 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001431, max 0.010707 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    976    979   81.6    0.1272   0.0970      0.0960

The atom 979 is the hydrogen atom on the phosphate. There has to be one
hydrogen atoms because it is protonated once. The other atom 976 is the
oxygen atom where the hydrogen atom is bound to.
The bounding parameters for this kind of binding were already there. I
didn't add them.

I already did it for another phosphorylation on another position in this
structure. And here I also got many LINCS errors. And again the problem is
the connection between the hydrogen atom and the oxygen atom.

But I do not understand why.
Can you please help me?!
>
>
> 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.
>
> Another thing worth considering - why do you necessarily need the rest of
> the
> structure to be identical?  Or perhaps better stated, why do you believe
> this to
> be the more appropriate model of reality?  Phosphorylation events
> frequently
> trigger structural changes in the protein, so I see no reason to assume it
> will
> have no effect on the rest of the structure.  At the very least, you can
> try a
> "normal" EM and MD procedure without freezing anything to see if you can
> determine the problem.  If things run normally without freezing, then you
> know
> that whatever you are doing here is artificial and problematic.
>
> -Justin
>
>> 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
>> ..
>>
>> Too many LINCS warnings (1000)
>>
>>
>> I already minimized the protein and everything was fine. There were no
>> errors:
>>
>> 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
>
> ========================================
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