AW: [gmx-users] question about the minimization
reisingere at rostlab.informatik.tu-muenchen.de
reisingere at rostlab.informatik.tu-muenchen.de
Thu Oct 18 14:51:44 CEST 2012
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.
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.
Best,
Eva
>
>
> 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
>>>>>>>
>>>>>>> --
>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>>>
>>> ========================================
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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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