AW: [gmx-users] question about the minimization

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Thu Oct 18 15:25:10 CEST 2012


Hi Justin,
I am sorry, I switched the radius and the numbers:
radius=0
charge=1
mass=1

But I already tried it without the membrane and there I had the same
problem. And also when I did not restrained anything. Not even the
membrane I got the high force and the LINCS warnings.

Of what physical problems do you think?

I already looked at the protein with Pymol and the residue with the high
force does not in interact with any other.

>
>
> On 10/18/12 8:51 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi Justin,
>>
>> Well I already tried the protein without the membrane and I got the same
>> result. And I also make sure that I had no error messages during the
>> preparation runs.
>>
>
> If the protein crashes in the absence of anything else, then likely you
> have
> problems with its starting geometry.  Applying restraints during
> minimization is
> probably causing the clashes to be insufficiently resolved.
>
>> I am using the amber03 force field.
>> My dummy atoms have a radius of 1.00 and a charge of 0.00. And yes they
>> are non bonded atoms.
>>
>
> Radius of 1.0 nm?  If the crash occurs without these atoms, then it's
> likely
> irrelevant, but with particles 10 times the size of normal atoms, you may
> be
> asking for trouble.
>
> -Justin
>
>
>>> On 10/18/12 7:05 AM, reisingere at rostlab.informatik.tu-muenchen.de
>>> wrote:
>>>> Hi Justin,
>>>>
>>>> I already read the page you send me.
>>>> And I am sure about the first points. But I am not completely sure
>>>> about
>>>
>>> Sure about the first five points?  The five suggestions on the page I
>>> linked are
>>> all diagnostic steps.  What did they turn up?
>>>
>>>> the mdp file for the nvt run.
>>>>
>>>> It looks like this:
>>>>
>>>> define               = -DPOSRES
>>>> integrator           = md
>>>> dt                   = 0.002
>>>> nsteps               = 10000
>>>> nstxout              = 0
>>>> nstvout              = 0
>>>> nstfout              = 0
>>>> nstlog               = 1000
>>>> nstxtcout            = 0
>>>> 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
>>>>
>>>
>>> What force field are you using?  What about my questions related to
>>> your
>>> so-called dummy atoms?  What are they and what are their parameters?
>>> Your
>>> minimization seemed fine, so there's clearly something wrong with the
>>> physical
>>> model that leads to a crash during MD.  At present, there's not enough
>>> information to say exactly what.
>>>
>>> -Justin
>>>
>>>>
>>>> Thank you for your help,
>>>>    Eva
>>>>
>>>>
>>>>>
>>>>>
>>>>> On 10/18/12 6:15 AM, reisingere at rostlab.informatik.tu-muenchen.de
>>>>> wrote:
>>>>>> Hi Erik,
>>>>>>
>>>>>> my .mdp file looks like this:
>>>>>>
>>>>>> define                  = -DPOSRES
>>>>>> integrator              = steep
>>>>>> emtol                   = 10
>>>>>> nsteps                  = 30000
>>>>>> 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
>>>>>>
>>>>>>
>>>>>> And yes, I use constraints. I have a membrane represented by dummy
>>>>>> atoms
>>>>>> around my protein. They are fixed and I also fixed the backbone. Or
>>>>>> is
>>>>>> that a problem.
>>>>>>
>>>>>
>>>>> The EM seems to have worked fine, so we need the .mdp file for NVT,
>>>>> not
>>>>> EM.
>>>>> Your membrane representation could be an issue, but I'm not clear on
>>>>> the
>>>>> terminology here.  A "dummy atom" (or virtual site) is a particle
>>>>> with
>>>>> nonbonded
>>>>> parameters but no mass.  Is that what you're dealing with?  If this
>>>>> membrane
>>>>> environment is fixed and the backbone is too, you may get clashes in
>>>>> the
>>>>> system,
>>>>> but it doesn't sound like there's a whole lot that's moving in the
>>>>> first
>>>>> place.
>>>>>     General troubleshooting advice (that I seem to post almost
>>>>> daily):
>>>>>
>>>>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>>>>>
>>>>> Your simulation is failing fairly early, so finding the source of the
>>>>> crash
>>>>> should not be terribly difficult.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>>>> It could be due to your mdp-settings. What's your time step? Do you
>>>>>>> use
>>>>>>> constraints and virtual interaction sites?
>>>>>>>
>>>>>>> Erik
>>>>>>>
>>>>>>> 18 okt 2012 kl. 12.04 skrev
>>>>>>> reisingere at rostlab.informatik.tu-muenchen.de:
>>>>>>>
>>>>>>>> Hi Felix,
>>>>>>>> thank you for your answer.
>>>>>>>> So you think that a force of 3.2341940e+02 is okey? To work on?
>>>>>>>>
>>>>>>>> I also tried to work on with a NVT run but then I got many many
>>>>>>>> LINCS
>>>>>>>> warnings:
>>>>>>>>
>>>>>>>> Step 1114, time 2.228 (ps)  LINCS WARNING
>>>>>>>> relative constraint deviation after LINCS:
>>>>>>>> rms 0.000169, max 0.001796 (between atoms 3480 and 3482)
>>>>>>>> bonds that rotated more than 30 degrees:
>>>>>>>> atom 1 atom 2  angle  previous, current, constraint length
>>>>>>>>      3480   3482   30.3    0.1090   0.1092      0.1090
>>>>>>>>
>>>>>>>> Step 1121, time 2.242 (ps)  LINCS WARNING
>>>>>>>> relative constraint deviation after LINCS:
>>>>>>>> rms 0.000108, max 0.000561 (between atoms 2000 and 2001)
>>>>>>>> bonds that rotated more than 30 degrees:
>>>>>>>> atom 1 atom 2  angle  previous, current, constraint length
>>>>>>>>      2002   2005   30.4    0.1090   0.1090      0.1090
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> And in the end there is the error:
>>>>>>>>
>>>>>>>> Fatal error:
>>>>>>>> 11 particles communicated to PME node 2 are more than 2/3 times
>>>>>>>> the
>>>>>>>> cut-off out of the domain decomposit
>>>>>>>> ion cell of their charge group in dimension x.
>>>>>>>>
>>>>>>>>
>>>>>>>> I looked it up on the GROMACS site and it was written there that
>>>>>>>> such
>>>>>>>> a
>>>>>>>> error is caused by a not well equilibrated system.
>>>>>>>>
>>>>>>>> So I thought that the high force might be the reason.
>>>>>>>>
>>>>>>>> What do you think?
>>>>>>>>
>>>>>>>> Thanks again!!
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi Eva,
>>>>>>>>>
>>>>>>>>> The change in energy in every step became smaller than the
>>>>>>>>> machine
>>>>>>>>> precision can represent (as is stated in the output). In other
>>>>>>>>> words:
>>>>>>>>> your
>>>>>>>>> system is minimized to a very high degree.
>>>>>>>>> A value of 10 for the Fmax is very low for a system like yours,
>>>>>>>>> even
>>>>>>>>> with
>>>>>>>>> a pure protein in water system you probably wouldn't hit this
>>>>>>>>> value.
>>>>>>>>> Furthermore, 30.000 steps for a minimization seems pretty high to
>>>>>>>>> me.
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>> Felix
>>>>>>>>>
>>>>>>>>> -----Ursprüngliche Nachricht-----
>>>>>>>>> Von: gmx-users-bounces at gromacs.org
>>>>>>>>> [mailto:gmx-users-bounces at gromacs.org]
>>>>>>>>> Im Auftrag von reisingere at rostlab.informatik.tu-muenchen.de
>>>>>>>>> Gesendet: Donnerstag, 18. Oktober 2012 10:56
>>>>>>>>> An: gmx-users at gromacs.org
>>>>>>>>> Betreff: [gmx-users] question about the minimization
>>>>>>>>>
>>>>>>>>> Hi everybody,
>>>>>>>>>
>>>>>>>>> I have a question about the minimization of my protein. For this
>>>>>>>>> minimization I fixed the backbone and the membrane atoms which
>>>>>>>>> around
>>>>>>>>> my
>>>>>>>>> protein.
>>>>>>>>>
>>>>>>>>> I minimized it 30000 steps long but after step 20385 it stops
>>>>>>>>> with
>>>>>>>>> the
>>>>>>>>> output:
>>>>>>>>>
>>>>>>>>> Steepest Descents converged to machine precision in 20385 steps,
>>>>>>>>> but
>>>>>>>>> did
>>>>>>>>> not reach the requested Fmax < 10.
>>>>>>>>> Potential Energy  = -8.8805600e+05
>>>>>>>>> Maximum force     =  3.2341940e+02 on atom 3050
>>>>>>>>> Norm of force     =  2.0930219e+00
>>>>>>>>>
>>>>>>>>> I do not see why it can not reach a lower force.
>>>>>>>>>
>>>>>>>>> I already looked at the structure with Pymol and there I saw that
>>>>>>>>> the
>>>>>>>>> atom
>>>>>>>>> 3050 is in a loop and do not interact with any other residue.
>>>>>>>>>
>>>>>>>>> My .mdp file looks like this:
>>>>>>>>>
>>>>>>>>> define                  = -DPOSRES
>>>>>>>>> integrator              = steep
>>>>>>>>> emtol                   = 10
>>>>>>>>> nsteps                  = 30000
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>> Do you see a reason why it can not reach a force lower than 10?
>>>>>>>>>
>>>>>>>>> Thank you,
>>>>>>>>> Eva
>>>>>>>>>
>>>>>>>>> --
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>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>>>>
>>>>>>> -----------------------------------------------
>>>>>>> Erik Marklund, PhD
>>>>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>>>>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>>>>>>> phone:    +46 18 471 6688        fax: +46 18 511 755
>>>>>>> erikm at xray.bmc.uu.se
>>>>>>> http://www2.icm.uu.se/molbio/elflab/index.html
>>>>>>>
>>>>>>> --
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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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
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
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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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>>
>>
>
> --
> ========================================
>
> 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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