[gmx-users] error during energy minimization
shailza singh
shailza_iitd at yahoo.com
Tue Feb 22 11:07:42 CET 2005
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?
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.
--- Itamar Kass <ikass at cc.huji.ac.il> wrote:
> Dear Shailza,
> I was wrong, if you get
> an error regarding
> pressure coupling you probably do MD and not energy
> minimization. In
> order to do EM change the line:
> integrator = md
> at the em.mdp file to
> integrator = cg
>
>
> Good luck.
>
>
> On Feb 22, 2005, at 11:23 AM, shailza singh wrote:
>
> >
> >
> > hi,
> > I am using Berendsen pressure coupling.
> >
> > shailza.
> >
> >
> >
> >
> > --- Itamar Kass <ikass at cc.huji.ac.il> wrote:
> >>
> >> Can you state what is your presser coupling
> >> method? Probably
> >> something is wrong with the pressure coupling.
> In
> >> case not, you can
> >> try to minimize your system using other coupling
> >> parameters.
> >> Kass.
> >>
> >>
> >> On Feb 21, 2005, at 6:16 PM, shailza singh wrote:
> >>
> >>>
> >>> hi all,
> >>> i am novice to GROMACS and trying to perform
> >> energy
> >>> minimization for my protein.But during mdrun i
> >>> encountered the following error:Back Off! I just
> >>> backed up step177.pdb to ./#step177.pdb.1#
> >>> Wrote pdb files with previous and current
> >> coordinates
> >>>
> >>> Step 179 Warning: pressure scaling more than
> 1%,
> >> mu:
> >>> inf inf inf
> >>> Warning: Only triclinic boxes with the first
> >> vector
> >>> parallel to the x-axis and the second vector in
> >> the
> >>> xy-plane are supported.
> >>> Box (3x3):
> >>> Box[ 0]={ inf,
> >> nan,
> >>> nan}
> >>> Box[ 1]={ nan,
> >> inf,
> >>> nan}
> >>> Box[ 2]={ nan,
> >> nan,
> >>> inf}
> >>> Can not fix pbc.
> >>> Fatal error: ci = -1 should be in 0 .. -1 [FILE
> >>> nsgrid.c, LINE 218]
> >>>
> >>> Please help
> >>> Thanking you in advance
> >>> shailja
> >>>
> >>>
> >>
> >
>
_______________________________________________________________________
> >>
> >>> _
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> >>
> >> ===========================================
> >> | 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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> >
>
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>
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>
> ===========================================
> | 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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