[gmx-users] Stuck ...
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 23 22:05:56 CEST 2007
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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