[gmx-users] LINCS warning in md run

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Thu Sep 20 12:52:13 CEST 2012


Hi,
 now I tried it without any restriction and still the LINCS warnings occur.
Since it is always the hydrogen atom where the huge force lies on I had
the idea just to remove the hydrogen atom to find out whether another atom
will occur to have such a high force on or everything went fine. And
indeed, without the hydrogen atom there is no problem during the MD run.
Even when I fix all the other atoms.

I can not see why this occurs. I already looked at the residue with pymol
and I could see that there is no other residue or atom clashing with it.

The residue looks like this:

ATOM    955  N   TYP    65      27.310  23.150  27.670  1.00  0.00        
  N
ATOM    956  CA  TYP    65      26.870  23.320  26.300  1.00  0.00        
  C
ATOM    957  C   TYP    65      27.920  23.760  25.300  1.00  0.00        
  C
ATOM    958  O   TYP    65      28.060  23.210  24.210  1.00  0.00        
  O
ATOM    959  CB  TYP    65      25.740  24.340  26.170  1.00  0.00        
  C
ATOM    960  CG  TYP    65      24.530  23.740  26.830  1.00  0.00        
  C
ATOM    961  CD1 TYP    65      24.410  23.760  28.220  1.00  0.00        
  C
ATOM    962  CD2 TYP    65      23.510  23.180  26.050  1.00  0.00        
  C
ATOM    963  CE1 TYP    65      23.290  23.210  28.840  1.00  0.00        
  C
ATOM    964  CE2 TYP    65      22.380  22.630  26.660  1.00  0.00        
  C
ATOM    965  CZ  TYP    65      22.260  22.630  28.070  1.00  0.00        
  C
ATOM    966  OH  TYP    65      21.160  22.100  28.670  1.00  0.00        
  O
ATOM    967  P   TYP    65      20.298  21.422  27.722  1.00  0.00        
  P
ATOM    968  OP1 TYP    65      21.003  21.245  26.467  1.00  0.00        
  O
ATOM    969  OP2 TYP    65      19.920  20.126  28.251  1.00  0.00        
  O
ATOM    970  OP3 TYP    65      19.106  22.218  27.498  1.00  0.00        
  O
ATOM    971  H   TYP    65      27.210  23.914  28.325  1.00  0.00        
  H
ATOM    972  HA  TYP    65      26.485  22.366  25.933  1.00  0.00        
  H
ATOM    973  HB1 TYP    65      25.524  24.543  25.119  1.00  0.00        
  H
ATOM    974  HB2 TYP    65      26.010  25.270  26.669  1.00  0.00        
  H
ATOM    975  HD1 TYP    65      25.154  24.234  28.821  1.00  0.00        
  H
ATOM    976  HD2 TYP    65      23.603  23.156  24.973  1.00  0.00        
  H
ATOM    977  HE1 TYP    65      23.200  23.222  29.916  1.00  0.00        
  H
ATOM    978  HE2 TYP    65      21.603  22.189  26.053  1.00  0.00        
  H
ATOM    979  H1P TYP    65      20.357  20.996  25.802  1.00  0.00        
  H


The topology entry in the aminoacid.rtp file looks like this:

[ TYP ]
 [ atoms ]
     N    N           -0.516300    1
    CA    CT           0.275503    2
    HA    H1           0.008223    3
    CB    CT          -0.354052    4
   HB1    HC           0.110326    5
   HB2    HC           0.110326    6
    CG    CA           0.119728    7
   CD1    CA          -0.198938    8
   HD1    HA           0.137143    9
   CE1    CA          -0.284884   10
   HE1    HA           0.177179   11
    CZ    C            0.452616   12
    OH    OS          -0.534452   13
     H    H            0.293600   14
   CE2    CA          -0.284884   15
   HE2    HA           0.177179   16
   CD2    CA          -0.198938   17
   HD2    HA           0.137143   18
     C    C            0.536600   19
     O    O           -0.581900   20
     P    P            1.393213   21
   OP1    OH          -0.752821   22
   OP2    O2          -0.822464   23
   OP3    O2          -0.822464   24
   H1P    HO           0.423316   25


[ bonds ]
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB   HB1
    CB   HB2
    CB    CG
    CG   CD1
    CG   CD2
   CD1   HD1
   CD1   CE1
   CE1   HE1
   CE1    CZ
    CZ    OS
    CZ   CE2
    OS     P
   CE2   HE2
   CE2   CD2
   CD2   HD2
     C     O
    -C     N
     P   OP1
     P   OP2
     P   OP3
   H1P   OP1


[ impropers ]
    -C    CA     N     H
    CA    +N     C     O
    CG   CE2   CD2   HD2
    CZ   CD2   CE2   HE2
   CD1    CZ   CE1   HE1
    CG   CE1   CD1   HD1
   CD1   CD2    CG    CB
   CE1   CE2    CZ    OH


The LINCS problems lie between the oxygen atom of the phosphate where a
hydrogen atom is bound to (OP1) and the hydrogen atom bound to the oxygen
atom of the phosphate (H1P).

Do you see where the problem lies?
Thank you,
 Eva

>
>
> On 9/18/12 8:58 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> 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
>
> Restraints during minimization generally restrict motion in the same way
> that
> freezing does.  Again, this is a potential barrier to sufficient
> minimization.
>
>> 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
>>
>
> Note that this outcome is even worse than before.  The maximum force is
> now over
> 10,000.
>
>>
>>
>>
>> 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
>>
>>
>
> As you should expect.  If you can't get a reasonable minimization, the MD
> will
> always crash.
>
>>
>> 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.
>
> Remove all restraints/freezing/whatever in the .mdp file and try the EM
> again.
> If it still does not converge to a reasonable value, then there are two
> potential problems:
>
> 1. The topology is flawed and thus the structure cannot be run stably
> 2. The structure cannot accommodate phosphate in this location and due to
> unresolvable clashes, the runs fail
>
> -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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