[gmx-users] Stuck ...
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu May 24 06:12:12 CEST 2007
Hi Stephane,
I think this ends up in treating symptoms. Setting up a simulation of
HIVP should not give such problems. It's probably best to start all
over: pdb2gmx, EM in vacuum, editconf -d 1.0, genbox, EM in solvent,
etc... Keep track of everything you're doing, give all files an
informative name and if you do run into the same trouble, zip up the
log (all command lines given and the output of each program) and all
the files (except .xtc .trr) and make these available through the web.
Cheers,
Tsjerk
On 5/23/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Stéphane Téletchéa wrote:
> > Mark Abraham a écrit :
> >> Stéphane Téletchéa wrote:
> >>> While switching from NVT to NPT, i'm crashing my simulation.
> >>>
> >>> The error message seen is (repeated 10 times, then mdrun aborts):
> >>> #####
> >>> Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20
> >>> -1.59647e+20 -1.59647e+20
> >>> Correcting invalid box:
> >>> old box (3x3):
> >>> old box[ 0]={-9.82630e+20, 0.00000e+00, -0.00000e+00}
> >>> old box[ 1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
> >>> old box[ 2]={ 0.00000e+00, 0.00000e+00, -1.12456e+21}
> >>> new box (3x3):
> >>> new box[ 0]={-9.82630e+20, 0.00000e+00, -0.00000e+00}
> >>> new box[ 1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
> >>> new box[ 2]={ 0.00000e+00, 8.90833e+20, -1.12456e+21}
> >>> .....
> >>> -------------------------------------------------------
> >>> Program mdrun_lam, VERSION 3.3.1
> >>> Source code file: ns.c, line: 265
> >>>
> >>> Fatal error:
> >>> Box was shifted at least 10 times. Please see log-file.
> >>> -------------------------------------------------------
> >>> #####
> >>>
> >>> I've searched in the archives this could be related to a non
> >>> sufficiently equilibrated system, but the first 20ps NVT run fine, so
> >>> i presume there's either a problem in the way i'm doing it (thus the
> >>> RFC-like question from the other message) or i'm missing something
> >>> obvious.
> >>>
> >>> Since i've tried to eliminate many errors and still get these errors
> >>> after different trials (removing shuffle and sort, generating or not
> >>> velocities while switching from pr1 to pr2, i've also tried the
> >>> "unconstrained_start=yes").
> >
> > Done
> >
> >> You will want to use unconstrained_start=yes in any restart of a
> >> simulation using constraints with which you're attempting to be exact.
> >>
> >>> If you have any pointer, i'll be very happy to read it ...
> >>>
> >>> I'm still looking at my setup system (protein in a water/spc solvent)
> >>> in order to find where is my error, but since the NVT run seems ok
> >>> (analysing precisely it at the moment, but no visual problem neither
> >>> any hint in the logs), i'm willing to understand why the switch to
> >>> NPT fails.
> >>
> >> As I think DvdS is hinting, if your box volume is such that the system
> >> is of the wrong size, then a sudden switch to NpT with a short time
> >> constant will cause a big perturbation to the system. This can break
> >> stuff. Check pressures, densities and volumes. To fix, either use a
> >> long time constant with NpT (and wait a while), or choose the volume
> >> with editconf so as to get the right outcome for the switch to NpT.
> >>
> >
> > I've tried all of them:
> > - adjusting box size (checking the *real* box size based on coordinates)
> > - using grouped tc-groups (protein+ligand and solvent+counter ions)
> > - increasing temperature/pressure coupling constants
> > - using unconstrained_start=yes systematically
> > - using a *big* cubic box (10*10*10nm) full of water molecules.
> > - i tried to use the single processor run instead of a parallel one
> >
> > But without luck ...
> >
> > Input files and setup protocol in French can be seen at:
> >
> > http://www.steletch.org/rpm/gromacs/
> >
> > The input files are basically based on the 1HPV.pdb HIV protease and
> > could serve as a good template for the wiki, i've a nearly completed the
> > procedure step, if the dynamics can be performed ... Only French to
> > English translation is lacking if the dynamic run works.
> >
> > I've included all the logs from the setup (including the minimisation)
> > and the result of the first pr1 (20ps) with logs, trajectory and edr (in
> > case i missed somthing obvious).
> >
> > The 1HPV has inside the 478 ligand but running the simulation with or
> > without has the same effect ...
> >
> > For some figures, here are what i see (and is obviously wrong) at the
> > end of the first PR run (so there's ne need fo run the PR1 step since
> > these values are completely out of reasonable range).
> >
> > #########################################################################
> > <====== ############################### ==>
> > <==== R M S - F L U C T U A T I O N S ====>
> > <== ############################### ======>
> >
> > Energies (kJ/mol)
> > G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> > 3.99578e+01 1.35925e+01 2.59496e+01 5.72270e-01 3.15990e+01
> > LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential
> > 6.64067e+03 2.73973e+00 2.15032e+04 2.45913e+02 1.55015e+04
> > Kinetic En. Total Energy Temperature Pressure (bar)
> > 8.79815e+03 2.38445e+04 1.09211e+01 2.81412e+30
> >
> > Total Virial (kJ/mol)
> > 8.23558e+31 8.69129e+29 1.16259e+30
> > 8.69129e+29 8.02947e+31 1.99268e+30
> > 1.16259e+30 1.99268e+30 9.15553e+31
> >
> > Pressure (bar)
> > 2.73510e+30 2.88645e+28 3.86106e+28
> > 2.88645e+28 2.66665e+30 6.61785e+28
> > 3.86106e+28 6.61785e+28 3.04062e+30
> >
> > Total Dipole (Debye)
> > 3.76515e+02 6.52877e+02 3.15905e+02
> >
> > Epot (kJ/mol) Coul-SR LJ-SR LJ-LR
> > Coul-14 LJ-14
> > Protein-Protein 2.71557e+01 1.68381e+00 2.61272e-01
> > 3.15990e+01 2.76596e-01
> > Protein-478 7.95930e-01 8.36554e-02 8.16916e-02
> > 0.00000e+00 0.00000e+00
> > Protein-SOL 4.14806e+02 1.00262e+02 4.10592e+00
> > 0.00000e+00 0.00000e+00
> > Protein-CL- 0.00000e+00 0.00000e+00 1.62381e-02
> > 0.00000e+00 0.00000e+00
> > 478-478 4.37839e-04 7.16249e-03 8.91323e-05
> > 5.73611e-04 2.96324e-01
> > 478-SOL 1.67881e+00 4.99479e+00 1.91387e-01
> > 0.00000e+00 0.00000e+00
> > 478-CL- 0.00000e+00 0.00000e+00 0.00000e+00
> > 0.00000e+00 0.00000e+00
> > SOL-SOL 2.17829e+04 6.64561e+03 4.03450e+00
> > 0.00000e+00 0.00000e+00
> > SOL-CL- 5.36674e+01 2.68157e+01 6.20907e-02
> > 0.00000e+00 0.00000e+00
> > CL--CL- 0.00000e+00 0.00000e+00 0.00000e+00
> > 0.00000e+00 0.00000e+00
> >
> > T-Protein_478 T-SOL_CL-
> > 2.09888e+01 1.09250e+01
> > #########################################################################
> >
> >
> > Please note that the simulated conformations were first minimsed and
> > converged to machine precision:
> > #########################################################################
> > Step= 4668, Dmax= 1.5e-06 nm, Epot= -1.65601e+06 Fmax= 2.52899e+03,
> > atom= 88783
> > Stepsize too small, or no change in energy.
> > Converged to machine precision,
> > but not to the requested precision Fmax < 10
> > #########################################################################
> >
> >
> > Really stuck with these and no clue :-(
> >
> > Thanks a lot for your advices and help,
> >
> > Stéphane
> your density is too high.
>
> try editconf -scale 0.9 0.9 0.9
> then minimize to get the bonds correct
> then md at low temperature
> then normal md
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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