[gmx-users] error during energy minimization

[shailza singh]

dear Itamar,
I used the following parameters for my protein :

title                    = Yo
cpp                      = /lib/cpp
include                  = -I../top
define                   = -DFLEX_SPC
integrator               = steep
nsteps                   = 50000
emtol                    = 500.0
emstep                   = 0.001


and received the following output:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 500

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy,
or turn
off constraints alltogether (set constraints = none in
mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 38
steps,
but did not reach the requested Fmax < 500.
Potential Energy  = -3.6378316e+05
Maximum force     =  2.7210256e+03 on atom 25146
Norm of force     =  1.7527736e+05

what does this Fmax < 500 means?I think the criterium
is also not set for the next step as Potential energy
should be:Potential Energy  = -1.19482e+05(online
reference)

Please help as I have performed this a number of times
but not being able to perform MD run.
thanking you in advance
shailza.




 --- Itamar Kass <ikass at cc.huji.ac.il> wrote: 
> 
> On Feb 22, 2005, at 12:07 PM, shailza singh wrote:
> 
> >
> > Dear Itamar,
> > I have one query... i am doing energy minimization
> of
> > the peptide in solvent..for that I followed the
> steps
> > as that given in getting-started Peptide in the
> > GROMACS  online reference.The em.mdp file (sample
> file
> > given in the online reference) has integrator as
> md
> > ...do I need to change it as cg?What I did was
> first
> > perform energy minimization of the peptide in
> > solvent..then short MD run and finally full MD
> run.Am
> > I proceeding in the right direction?or Do i need
> to
> > change the integator as cg?
> >
> 
> Hi shailza, the steps you stated seems fine to me,
> but I am working on 
> in membrane peptide. Any how, in order to do EM you
> should use cg 
> integrator.  For example:
> define              =  -DFLEX_SPC
> integrator           =  cg
> nsteps               =  50000
> ;       Energy minimizing stuff
> emtol                =  500.0
> emstep               =  0.001
> 
> Later on, you should do short MD run in which the
> peptide atoms are 
> restrained, for example:
> integrator           =  md
> dt                   =  0.002	; ps !
> nsteps               =  250000	; total 0.5s.
> ; Constrain control
> define               = -DPOSRES
> constraints          = all-bonds
> The flag -DPOSRES indicate you use the position
> restrains given in the 
> itp file (e.g. posre_A.itp) created by pdb2gmx. 
> Later on run a longer 
> simulation without position restrains.
> 
> > My second question is :I changed both the
> temperature
> > coupling and pressure coupling ...and I got
> > step 960, will finish at Tue Feb 22 16:46:00
> > 2005Warning: 1-4 interaction between 1528 and 1533
> at
> > distance larger than 1 nm
> > These are ignored for the rest of the simulation
> > turn on -debug for more information
> >
> > Step 961, time 1.922 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > max 0.019805 (between atoms 1531 and 1532) rms
> > 0.000548
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current,
> constraint
> > length
> >    1531   1532   51.8    0.9733   0.0980     
> 0.1000
> >
> > Step 962, time 1.924 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > max 3.965767 (between atoms 1531 and 1532) rms
> > 0.106540
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current,
> constraint
> > length
> >    1531   1532   90.0    0.0980   0.4966     
> 0.1000
> >    1531   1533   90.0    0.0996   0.4604     
> 0.1000
> > After this its running fine.
> > Please tell me as to where am i doing wrong?
> > thanking you in advance
> > shailza.
> >
> 
> This is probably due to some defect in your starting
> structure, maybe a 
> collision between atoms or like.  If it ends fine it
> O.K..  Again, what 
> you did was MD and not EM, I guess that doing EM
> first will prevent 
> this kind of problems.
> 
> 
>       Good luck, Itamar.
> 
> 
> ===========================================
> | Itamar Kass
> | The Alexander Silberman
> | Institute of Life Sciences
> | Department of Biological Chemistry
> | The Hebrew University, Givat-Ram
> | Jerusalem, 91904, Israel
> | Tel: +972-(0)2-6585194
> | Fax: +972-(0)2-6584329
> | Email: ikass at cc.huji.ac.il
> | Homepage: 
>
http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> ============================================
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