[gmx-users] neighborsearching in semiisotropic systems

Till Rudack till at bph.rub.de
Tue Jun 3 17:53:44 CEST 2008 

The system is also well equilibrated and works fine with single precision.
This is the mdp file of the run that crashed:
title           =       test MD double
cpp             =       /lib/cpp
integrator      =       md
pbc             =       xyz
ns_type         =       grid
dt              =       0.002
nsteps          =       5000000
nstlist         =       5
nstcomm         =       1
nstlog          =       5000
nstenergy       =       1000
nstxtcout       =       1000
nstxout         =       1000
nstvout         =       1000
nstfout         =       1000
coulombtype     =       PME
rlist           =       0.9
rcoulomb        =       0.9
rvdw            =       1.4
fourierspacing  =       0.12
pme_order       =       4
ewald_rtol      =       1E-5
tcoupl          =       berendsen
tc-grps         =       System
tau_t           =       0.1
ref_t           =       298.15
pcoupl          =       berendsen
pcoupltype      =       semiisotropic
tau_p           =       0.5    0.5
compressibility =       4.5E-5 4.5E-5
ref_p           =       1      1
gen_vel         =       yes
gen_temp        =       298.15
gen_seed        =       173529
constraints     =       all-bonds
constraint_algorithm =  lincs

And if I took the same minimized and equilibrated structure and change 
only from semiisotropic to isotropic

pcoupl          =       berendsen
pcoupltype      =       isotropic
tau_p           =       0.5
compressibility =       4.5E-5
ref_p           =       1

the error does not occur anymore.

Till

Justin A. Lemkul schrieb:
> How about equilibration?  Your first message mentioned that you might suspect a
> water molecule is to blame.  Did you restrain the peptide and perform any sort
> of NVT or NPT ensemble to equilibrate your solvent?  It might also be useful to
> see your full .mdp file in case we might be able to spot any errors.
> 
> -Justin
> 
> Quoting Till Rudack <till at bph.rub.de>:
> 
>> Dear Justin,
>> the system is well minimized. I performed a steepest descent
>> minimization followed by a conjugate gradient minimization and then
>> minimize it again with steepest descent. The problem occurred after 3ns
>> or in the second run after 5ns so I do not think it is a problem of
>> minimization .
>> Till
>>
>> Justin A. Lemkul schrieb:
>>> Did you do any sort of minimization or equilibration on your system?
>> Usually
>>> these errors arise because of a poor starting structure, or one that has
>> been
>>> insufficiently equilibrated.
>>>
>>> -Justin
>>>
>>> Quoting Till Rudack <till at bph.rub.de>:
>>>
>>>
>>>> Dear users,
>>>>
>>>> During protein simulations occurred the range checking error of the
>>>> neighborsearching. I checked the comments on this mistake in the user
>>>> list and then checked my system on any hints of an exploding system but
>>>> it seems to be stable. In order to be sure I cut down the system to a
>>>> small peptide consisting of only ten aminoacids and used the ffG43a1
>>>> forcefield.
>>>>
>>>>
>>>> I performed 10ns simulations of this small system in a cubic
>>>> spc-waterbox with different pressure parameters and tried single and
>>>> double precision. I got the following results:
>>>>
>>>>
>>>> For
>>>>
>>>> pcoupltype = semiisotropic
>>>>
>>>> tau_p = 0.5 0.5
>>>>
>>>> compressibility = 4.5E-5 4.5E-5
>>>>
>>>> ref_p = 1 1
>>>>
>>>>
>>>> with double precision occurred the mistake:
>>>>
>>>>
>>>> -------------------------------------------------------
>>>>
>>>> Program mdrun_d.mpi, VERSION 3.3.1
>>>>
>>>> Source code file: nsgrid.c, line: 226
>>>>
>>>>
>>>> Range checking error:
>>>>
>>>> Explanation: During neighborsearching, we assign each particle to a grid
>>>>
>>>> based on its coordinates. If your system contains collisions or parameter
>>>>
>>>> errors that give particles very high velocities you might end up with some
>>>>
>>>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>>>>
>>>> put these on a grid, so this is usually where we detect those errors.
>>>>
>>>> Make sure your system is properly energy-minimized and that the potential
>>>>
>>>> energy seems reasonable before trying again.
>>>>
>>>>
>>>> Variable ci has value 284. It should have been within [ 0 .. 200 ]
>>>>
>>>> Please report this to the mailing list (gmx-users at gromacs.org
>>>> <mailto:gmx-users at gromacs.org>)
>>>>
>>>>
>>>> Then, I changed tau_p to 5.0 and the mistake did not occurce anymore
>>>> during the 10 ns. With single precision the mistake never occurres. I
>>>> also tested double precision with pcoupltype = isotropic and this also
>>>> works.
>>>>
>>>> Next, I wanted to reproduce the mistake so I took the same tpr file of
>>>> the crashed simulation with tau_p = 0.5 and started the simulation
>>>> again. The mistake occurred again but not at the same timestep. The
>>>> first run crashed after step 1558630 and the second run after step
>>>> 2597500 and also the ci variable is not exactly the same (Variable ci
>>>> has value 283. It should have been within [ 0 .. 200 ]).
>>>>
>>>>
>>>> I think there might be a problem between the neighborsearching and the
>>>> semiisotropic pressurcoupling together with double precision. I am quite
>>>> sure that the peptide is not the problem. Maybe there is a problem with
>>>> a water molecule. I would be glad if someone can give me an explanation
>>>> why this mistake is not reproducable at the same timestep and why it
>>>> occures with tau_p=0.5 and not with tau_p=5.0.
>>>>
>>>>
>>>> Thanks
>>>>
>>>>
>>>> Till
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>
>>>
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul at vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>>
>>> ========================================
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> 
> 
> 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> 
> ========================================
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