Re: FATAL ERROR: unknown floating-point error, errno = 4

From: Manori Indira Jayasinghe (
Date: Fri Dec 23 2005 - 11:47:10 CST

Dear Chris,
Thank you for your comments and I think I need to figure out the proper
values for these variable to suit my system.I will give some details of
what I am doing. I am simulating a freenergy profile of a molecular
with 100 atoms namely Uranyl Nitrate Tri Butyl Phosphate at water
(874)/hexane(143) interface. In my system I have 3 interfaces,
water/water vapor, water/hexane, hexane/hexane vapor.I use mmfp in charmm
to prevent hexane and water penetrating out of the unit cell. But I
havent done anything like that in namd.I am running this
system in Charmm Umbrella sampling module and it runs fine except one
problem. RXNCOR in charmm is not recomended for parallel runinng and it
take for one window 3 Angstrom for 500 ps about 2 and half days, which is
qiute long I think . I use 0.7 Kcal/mole for the force constant in
RXNCOR.I was able to do 2 windows for 500 ps each the free
enrgy profiles looks fine. I need to switch my system to namd abf, hence I can get it run parallel and my
simulation will be faster.Do you have any sujestions for those variables.
Thank you very much. Manori

 On Fri, 23 Dec 2005, Chris Chipot wrote:

> Manori,
> could you, please, provide me with additional detail about the system
> you are running?
> In the meantime, I can comment on the values that you used in the ABF
> section of your input file:
> abf dxi 0.04
> abf forceConst 0.1
> abf applyBias yes
> abf fullsamples 20
> The choice of dxi depends on how fast the free energy varies. 0.04 Å
> is what I would use for a very fast changing free energy profile.
> The forceconst variable controls the walls at the border of the path
> you are sampling. 0.1 kcal/mol/Ų constitutes an excessively weak
> restraint unlikely to prevent sampling to go beyond the bounds defined
> by ximin and ximax.
> More worrisome, too small a value of fullsamples is prone to drive
> your system out of equilibrium. Keep in mind that the samples are
> accrued in dxi-wide bins prior to application of -?F??? ??. In other
> words, fullsamples controls the convergence of ?F???. It is inherently
> system-dependent and varies as a function of how fast the different
> degrees of freedom relax. Too small a value of fullsamples is
> equivalent to applying an erroneous average force that will often
> overshoot the barriers of the free energy landscape.
> Chris Chipot
> _______________________________________________________________________
> Chris Chipot, Ph.D.
> Equipe de dynamique des assemblages membranaires
> Unité mixte de recherche CNRS/UHP No 7565
> Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
> B.P. 239 Fax: (33) 3-83-68-43-87
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> _______________________________________________________________________

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