Dear Gromacs users, <br> <br> I am using tabulated potentials for dihedrals of my system which is of form dih = (1/2)*K[COS n(phi-phi0)], Here n=3.<br> I have generated table_d0.xvg by uniformly varying "phi" as 0.1 from -180 to 180 and calculated the numerical derivative and force by using the relations <br>
der = Y(n+1)- Y(n-1)/ (2*h) ; force = -der ; Here h = step size (i.e 0.1 in my case).<br> Here I have some doubts:<br>1) Am I using the correct relations for calculation of derivative and force. <br>2) which value should we take for the k ( force constant) in ffbonded.itp, the value of " k " that specified with the dihedral potential ? or some arbitrary number ? <br>
As I have used the value of "k" given with the dihedral function in calculations of potential and the force, Is it necessary to mention force constant value again in ffbonded.itp and <br>3) if I run mdrun as<br>
mdrun -tableb table_do.xvg it giving the error : "Library file table_d0_d0.xvg not found in current dir nor in default directories."<br>Can you please suggest me the correct way of using the -tableb option in the case of multiple tables.<br>
<br>Thank you in advance,<br><br>Regards,<br>Ramesh Cheerla.<br>