[gmx-users] Tabulated potentials for the Dihedrals - regd
ramesh cheerla
rameshgromacs at gmail.com
Wed May 16 20:16:43 CEST 2012
Dear Gromacs users,
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.
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
der = Y(n+1)- Y(n-1)/ (2*h) ; force = -der ; Here h = step size (i.e 0.1
in my case).
Here I have some doubts:
1) Am I using the correct relations for calculation of derivative and
force.
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 ?
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
3) if I run mdrun as
mdrun -tableb table_do.xvg it giving the error : "Library file
table_d0_d0.xvg not found in current dir nor in default directories."
Can you please suggest me the correct way of using the -tableb option in
the case of multiple tables.
Thank you in advance,
Regards,
Ramesh Cheerla.
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