AW: [gmx-users] question about the minimization

[Erik Marklund]

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