AW: AW: [gmx-users] question about the minimization
reisingere at rostlab.informatik.tu-muenchen.de
reisingere at rostlab.informatik.tu-muenchen.de
Thu Oct 18 16:48:47 CEST 2012
I have a cap "ACE" in the beginning of the protein but this was also
defined in the aminoacids.rtp file in the amber03 forcefield
> If you got the same problems with the protein only (and without any
> restraints), I wonder if you have any non-standard residues (i.e. ligands
> or protein modifications) present in your system?
> Because a normal protein should work just fine with the parameters you
> gave us.
>
> -----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 15:28
> An: Discussion list for GROMACS users
> Betreff: Re: AW: [gmx-users] question about the minimization
>
> 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#Diagno
>>>>>> sing_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
>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>>>>>>> --
>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>> * Please search the archive at
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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
>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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>
>
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