[gmx-users] dihedral MM scan

[Mohsen Ramezanpour]

Dear Gromacs users,

I want to do a MM scan on a dihedral and compare with the available QM
profile using Gromacs 5.1.3

I used the following (updated compared to my last email on parameters)
em.mdp and md.mdp files for relaxation and zero-step md, respectively.

*em.mdp:*
define                     = -DPOSRESDIH
integrator                 = steep
emtol                       = 100.0
nsteps                     = 50000
vdwtype                   = Cut-off
vdw-modifier            = none
coulombtype             = Cut-off
constraints                = h-bonds
constraint_algorithm    = LINCS
nstlist                        = 0
ns-type                      = simple
pbc                           = no
cutoff-scheme           = group
rcoulomb                   = 0
rvdw                         = 0
rvdw_switch             = 0
rlist                            = 0

Which, by -DPOSRES I am applying position restraint on specific dihedral of
interest.
The following lines were included at the end of molecule.itp

#ifdef POSRES

[ dihedral_restraints ]

 1    18  8   9     1   120   0   10000

#endif



*as for md.mdp:*
define                  =
integrator              = md
dt                        = 0.001
nsteps                  = 0
nstlog                  = 0
nstxout                 = 0
nstvout                 = 0
nstfout                  = 0
nstcalcenergy           = 0
nstenergy                 = 0
nstxout-compressed      = 100000
compressed-x-precision  = 1000
coulombtype                  = Cut-off
vdwtype                         = Cut-off
vdw-modifier                   = none
constraints                     = h-bonds
constraint_algorithm        = LINCS
nstcomm                         = 100
comm_mode               = linear
comm_grps                 = system
refcoord_scaling           = com
nstlist                          = 0
ns-type                        = simple
pbc                            = no
cutoff-scheme              = group
rcoulomb                = 0
rvdw                      = 0
rvdw_switch            = 0
rlist                         = 0
continuation            = yes

It seems to work fine, at least because grompp do not complain and it gives
me the desired files.

There is one problem:
Looking at the Potential Energy which zero-step md for angle = 120 gives me
a value of 384.682 KJ/mol (ca. 91 Kcal/mol) which is almost 20 times the
value from QM profile (4.5 Kcal/mol) by GAAMP server (as I understood, the
units for dihedral profiles by GAAMP are in Kcal/mol).

I used the parameters GAAMP gave me (partial charges and dihedral
parameters).

Briefly, the same molecule which I uploaded to GAAMP was used for MM scan
in vaccume. No box and infinite cutoff was used. I did an EM step by above
em.mdp and let the system to relax. Then, I removed the restraints and did
the zero-step md part and got this energy.

It is worth mentioning that the molecule is positively charges. BUT, as I
understood, this is what GAAMP also uses for the QM scan.

What could be the problem?

I highly appreciate your comments as expert in this.

Cheers
Mohsen



-- 
*Rewards work better than punishment ...*