AW: [gmx-users] question about the minimization
Erik Marklund
erikm at xray.bmc.uu.se
Thu Oct 18 13:37:26 CEST 2012
This is not an NVT run. This is EM. Furthermore, I don't see the point in combining position restraints with EM.
Erik
18 okt 2012 kl. 12.15 skrev reisingere at rostlab.informatik.tu-muenchen.de:
> 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.
>
> Thank you ,
> Eva
>
>
>> 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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>>>
>>>
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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
>>
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>
>
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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
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