R: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem

albitauro at virgilio.it albitauro at virgilio.it
Thu Oct 8 15:58:41 CEST 2009

Hi Berk,
the potential I used comes indeed from Boltzmann inversion but I fitted it with a polynomial function of suitable degree which gave an almost perfect agreement on the range chosen (outside this range it reproduces the correct repulsive branches of the potential).  I generated the tabulated potential on the basis of this polynomial fitting and also the derivatives in the third coulmn of the table were calculated on the basis of the analytical derivative of the polynomial. Therefore, all the numerical noise has been removed. Maybe, are there numerical problems of any kind if the potential has a very large repulsive value on the repulsive branches? I any  case in my initial configuration all the bonds share value near the minimum and so they are not exploring these highly repulsive regions.
Thank you


----Messaggio originale----

Da: gmx3 at hotmail.com

Data: 8-ott-2009 9.12 AM

A: "Discussion list for GROMACS users"<gmx-users at gromacs.org>

Ogg: RE: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential -	Problem



The required spacing is basically only related with the second derivative of the potential
and the accuracy you want. In "standard" cases, your spacing of 0.001 nm should be enough.
But if your potential comes from some numerical inversion procedure, your potential could
be very noisy, which could result in nearly random forces, which could cause the system to crash.
Also the maximum time step you can take will depend on the second derivative of the potential.


Date: Thu, 8 Oct 2009 11:01:39 +0200
From: albitauro at virgilio.it
To: gmx-users at gromacs.org
Subject: R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential -	Problem


I used gmxcheck and gxmdump to compare the results of two simulations on an identical system but using two different tabulated potential, one harmonic (the simulation ended correctly) and one not. There are no differences in terms of non bonded interactions, other energy terms and the parameters of the simulation.
Therefore, it is still something related to the tabulated potential. Is there a minimum or a maximum number of (uniformly spaced) points suggested (or required) for a tabulated potential? In this case I used 1001 points to sample an interval from 0 to 1.0 nm. 
Many thanks,


----Messaggio originale----
Da: Mark.Abraham at anu.edu.au
Data: 5-ott-2009 11.19 PM
A: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
Ogg: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem

albitauro at virgilio.it wrote:
> Hi,
> I came back to my original stretching potential in tabulated form and I 
> have still problems...
> when running a geometry optimization the results are like that:
> **************************************************+
> ^MStep 635, Epot=2.259501e+02, Fnorm=4.086e+00, Fmax=1.886e+01 (atom 34)
> ^MStep 636, Epot=2.259499e+02, Fnorm=3.847e+00, Fmax=1.992e+01 (atom 33)
> ^MStep 637, Epot=2.259495e+02, Fnorm=1.002e+01, Fmax=5.408e+01 (atom 33)
> ^MStep 638, Epot=2.259449e+02, Fnorm=1.026e+01, Fmax=4.098e+01 (atom 34)
> ^MStep 639, Epot=2.259393e+02, Fnorm=2.193e+01, Fmax=1.159e+02 (atom 35)
> ^MStep 640, Epot=2.259364e+02, Fnorm=1.469e+01, Fmax=7.064e+01 (atom 34)
> ^MStep 641, Epot=2.259335e+02, Fnorm=1.281e+01, Fmax=7.154e+01 (atom 34)
> ^MStep 642, Epot=2.259315e+02, Fnorm=5.803e+00, Fmax=2.861e+01 (atom 35)
> ^MStep 643, Epot=2.259314e+02, Fnorm=6.332e+00, Fmax=3.116e+01 (atom 34)
> ^MStep 644, Epot=2.259310e+02, Fnorm=3.550e+00, Fmax=1.502e+01 (atom 34)
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 0.1
> ************************************************************************************
> as if the system is frozen. My system here is an isolated, linear and 
> finite-length chain.
> When running an md simulation I got the error:
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: bondfree.c, line: 1772
> Fatal error:
> A tabulated bond interaction table number 0 is out of the table range: r 
> 1.815411, between table indices 1815 and 1816, table length 1001
> -------------------------------------------------------
> The tabulated potential is uniformly spaced, the bond type is 8 to 
> exclude LJ interaction between bonded atoms, nrexcl=1 to include 1-3 
> interactions (as required by MARTINI force field). 

That seems like it should work.

> The same system does 
> not have any problem when running simulation with an harmonic stretching 
> potential in both numerical and analytical form.
> Does anyone have any suggestion for possible solutions or error in the 
> input?

Running gmxcheck between various .tpr files may be instructive, e.g. one 
file may have many more nonbonded interactions, or such. Otherwise, 
posting your .mdp file and the start of your .top may help us spot a 

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