AW: [gmx-users] question about the minimization
Justin Lemkul
jalemkul at vt.edu
Thu Oct 18 12:26:09 CEST 2012
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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>>>
>>>
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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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>
>
--
========================================
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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