[gmx-users] LINCS warning in md run

Thu Sep 13 10:22:52 CEST 2012

Hi Justin,

this atom is the CG atom of the phosphate I added to the protein.
But how can I find out by what it is punished?

This is the topology for this residue in the aminoacid.rtp file. I added
it manually. The parameter are from the amber parameter database
(http://www.pharmacy.manchester.ac.uk/bryce/amber/):

[ 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
   OP1   H1P

[ 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

Additionally I had to add an entry in the ffbonded file in the part [
dihedraltypes ]

CA  CA  C   OS       4      180.00     4.60240     2    ;

Here I am not completely sure about the entry because I could not find a
source for this combination of atoms.
But there is already an entry for the combination
CA  CA  C OH
Which has the same parameters.
Could this be the problem?

And if it could be, can you please give me hint where I can find
parameters for it? Because I really could not find it.

Thank you,
Eva

>
>
> On 9/12/12 3:39 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi Justin,
>> my 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  System_&_!Protein
>> tau_t           = 0.1     0.1
>> ref_t           = 298     298
>> pcoupl          = no
>> freezegrps = Protein_&_!TYP
>> freezedim = Y Y Y
>>
>>
>> I added a phosphate (TYP) to my protein and now want to do first a
>> minimization (which I already did), then a short md run (for the case
>> that
>> I am in a local minima) and after that again a minimization.
>> Since I only want to minimize the energy of the phosphate I freezed the
>> rest of the protein (Protein_&_!TYP).
>>
>>
>> Since on my cluster I am not allowed to run long jobs I had to divide
>> the
>> minimization run in several runs. The output of the last run was:
>>
>> Steepest Descents converged to machine precision in 15 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy  = -7.7264606e+05
>> Maximum force     =  1.6227990e+04 on atom 961
>> Norm of force     =  1.2328220e+02
>>
>> gcq#192: "It's So Fast It's Slow" (F. Black)
>>
>>
>> Steepest Descents converged to machine precision in 15 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy  = -7.7264606e+05
>> Maximum force     =  1.6227990e+04 on atom 961
>> Norm of force     =  1.2328220e+02
>>
>>
>> After this minimization run I wanted to do the md run.
>>
>> My protein is a membrane protein with its surrounding membrane. I
>> already
>> did a minimization and md run with this protein but without the
>> phosphate.
>> The only difference to the time when everything worked fine is the
>> phosphate.
>>
>> Does this help you somehow to see the failure?
>>
>
> Your minimization is insufficient.  You have a maximum force in excess of
> 16000
> on atom 961.  Such a large force explains the crash.  You should
> investigate
> what this atom is and what is pushing on it so hard.
>
> -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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