AW: [gmx-users] question about the minimization
reisingere at rostlab.informatik.tu-muenchen.de
reisingere at rostlab.informatik.tu-muenchen.de
Thu Oct 18 14:46:56 CEST 2012
Hi Erik,
this is my .mdp file:
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
The file you respond to was from the EM run.
> 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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