Hello Justin,
Thanks for the response. In the EMP2 model the bond angle potential is of
the harmonic form with the equilibrium angle 180. The only way I could
include this in the .itp was though [angles].
The other two options [angle_restraints] and [angle_restraints_z] has a
different form for
Hello Justin,
I performed energy minimization , the way you performed for the free
energy calculation for the methane-water system in the tutorial. In the
first step steepest descent was used followed by l-bfgs. The emtol (force)
was set to 10 kj/mol/nm.
The final results can be summerized as:
Hello,
Thank you both for the comments. I am using gromos96 forcefield . I read
a little bit and as you said the nonbonded cutoff has to be higher.
The tau_p=5ps was chosen , since the manual mentions that the value has to
be raised by 4-5 times on going from berendsen to parrinello-rahman
bar
