[gmx-users] Tabulated non-bonded potentials - regd

ramesh cheerla rameshgromacs at gmail.com
Tue Apr 23 11:29:59 CEST 2013

Dear Gromacs users,

      In forcefield of  my system, I have non-bonded function of the form U
= A*exp(-Brij) - C/(rij^6) - D/(rij^4),  for this I wanted to use tabulated
potentials. I have defined functions f(r), g(r) and  h(r)  as the following,
f = 1/r;
fprime = 1/(pow(r,2));
g = (C*(-1/(pow(r,6))));
gprime = (-6*C/(pow(r,7)));
h = A*exp(-B*r);
hprime = ((A*B)*(exp(-B*r)));
      Then I have tabulated all these  with a bin size (dr) of 0.002 nm and
given "nbfunc" as 1 in forcefield.itp and provided "C" and "A" as 1 in
ffnonbonded.itp (As I have used A,B & C values in generation of table
itself) . I have generated one such table for each  interaction.  While
running simulations with these tables  I am getting the following warning:

"WARNING: For the 3999 non-zero entries for table 2 in table.xvg the forces
deviate on average 78% from minus the numerical derivative of the potential"
After this job is crashing with error  "Segmentation fault"
1) Can anybody please tell me the reason for the above Warning  and how one
can rectify it ?
2) Can I define the functions for the above mentioned  non-bonded function
like this ?
I have checked potential energy of model system (single point energy
calculations i.e., zero step MD and the one that  obtained from the code
that I have written, both are matching.
I am using GROMACS version 4.5.5 and also tested the same thing in V 4.6.

Can anybody help me in this regard,

Thank you in advance.


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