Dear all,
I have a question concerning tabulated potentials:
My System consists of three different particles P_1, P_2 and P_3 and I would like to use
tabulated potentials for the bonded as well as the nonbonded interactions.
Runing mdrun produces both:
1.) various warnings:
WARNING: For the 239 non-zero entries for table 0 in table_P_1_P_1.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 168 non-zero entries for table 1 in table_P_1_P_1.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 168 non-zero entries for table 1 in table_P_1_P_2.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 168 non-zero entries for table 1 in table_P_1_P_3.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 168 non-zero entries for table 1 in table_P_2_P_2.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 168 non-zero entries for table 1 in table_P_2_P_3.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 168 non-zero entries for table 1 in table_P_3_P_3.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 199 non-zero entries for table 0 in table_b0.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 199 non-zero entries for table 0 in table_b1.xvg the forces deviate on average 244% from minus the numerical derivative of the potential
WARNING: For the 199 non-zero entries for table 0 in table_b2.xvg the forces deviate on average 165% from minus the numerical derivative of the potential
WARNING: For the 179 non-zero entries for table 0 in table_a0.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 179 non-zero entries for table 0 in table_a1.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 179 non-zero entries for table 0 in table_a2.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 177 non-zero entries for table 0 in table_a3.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 358 non-zero entries for table 0 in table_d0.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 356 non-zero entries for table 0 in table_d1.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 358 non-zero entries for table 0 in table_d2.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 358 non-zero entries for table 0 in table_d3.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 356 non-zero entries for table 0 in table_d4.xvg the forces deviate on average 196% from minus the numerical derivative of the potential
WARNING: For the 168 non-zero entries for table 1 in table_P_3_P_3.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 199 non-zero entries for table 0 in table_b0.xvg the forces deviate on average 164% from minus the numerical derivative of the potential
WARNING: For the 199 non-zero entries for table 0 in table_b1.xvg the forces deviate on average 244% from minus the numerical derivative of the potential
WARNING: For the 199 non-zero entries for table 0 in table_b2.xvg the forces deviate on average 165% from minus the numerical derivative of the potential
WARNING: For the 179 non-zero entries for table 0 in table_a0.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 179 non-zero entries for table 0 in table_a1.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 179 non-zero entries for table 0 in table_a2.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 177 non-zero entries for table 0 in table_a3.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 358 non-zero entries for table 0 in table_d0.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 356 non-zero entries for table 0 in table_d1.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 358 non-zero entries for table 0 in table_d2.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 358 non-zero entries for table 0 in table_d3.xvg the forces deviate on average 193% from minus the numerical derivative of the potential
WARNING: For the 356 non-zero entries for table 0 in table_d4.xvg the forces deviate on average 196% from minus the numerical derivative of the potential
2.) and a segmentation fault:
step 0 segmentation fault.
My question:
Why is there so much deviation between the forces, calculated by gromacs and the numerical deviative of the potential?
I have no impact on that calculation, does I?
The values of the force specified in the table are right for sure.
It is possiible that the segmentation fault results from this "force-problem" is it?
Tank you very much in advance.
Best,
Liz
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