[gmx-users] binding free energy with gromacs2016

[Qasim Pars]

Dear users,

I will try to do binding free energy calculation using GROMACS2016 but I am
confused a little bit about the preparation of  the input files. I have a
few questions:

1) There are below lines to apply a harmonic distance restraint in the mdp
files of the binding free energy tutorial
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

pull           = umbrella
pull_geometry  = distance
pull_dim       = Y Y Y
pull_start     = no
pull_init1     = 0.654
pull_ngroups   = 1
pull_group0    = a_1391
pull_group1    = a_2615
pull_k1        = 0.0   ; kJ*mol^(-1)*nm^(-2)
pull_kB1       = 4184  ; kJ*mol^(-1)*nm^(-2)

Question 1: Instead of those lines I would like to use the [
intermolecular_interactions ] section in the topology file with
GROMACS2016. Could you please tell me what to write the [
intermolecular_interactions ] section?

2) complex.top file of the tutorial is as follows:
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

[ atomtypes ]
;name  bond_type          mass        charge  ptype   sigma      epsilon
c3            c3          0.0000      0.0000  A   3.39967e-01  4.57730e-01
dc3           c3          0.0000      0.0000  A   0.00000e+00  0.00000e+00
....

Question 2: Why all values (sigma and epsilon) of dc3 are zero?

[ nonbond_params ]
; i  j    func  sigma           epsilon
c3   c3    1     3.3996700e-01   4.5773000e-01
dc3  dc3   1     3.3996700e-01   4.5773000e-01
....
Question 3: Why all values of dc3 aren't zero?

[ angle_restraints ]
; ai     aj    ak    al    type     thA      kA         multA      thB
 kB         multB
 1393   1391   2615  1391  1        88.8     0.00       1          88.8
41.84   1
 1391   2615   2614  2615  1        32.9     0.00       1          32.9
41.84   1

[ dihedral_restraints ]
; ai    aj    ak    al       type   phiA     dphiA   kA          phiB
dphiB   kB
  1410  1393  1391  2615     1      -159.7  0.0      0.00        -159.7
0.0     41.84
  1393  1391  2615  2614     1      122.6   0.0      0.00         122.6
0.0     41.84
  1391  2615  2614  2610     1      12.8    0.0      0.00          12.8
0.0     41.84
.....
Question 4: Do I still need to put those ligand parameters (dc3, [
angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to
use with GROMACS2016?

I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't
understand how to prepare the input files.
-- 
Qasim Pars