[gmx-users] NVT.mdp running in 4.6 version but failed in VERSION 5.1.2

[Rana Ali]

Hi
I was running water on graphene using PBC =xy  by keeping the graphene
fixed in y direction.
It was running in gromacs version 4.6 but failed to run in 5.1.2.
This is the error.
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#

ERROR 1 [file nvt.mdp]:
  With Verlet lists only full pbc or pbc=xy with walls is supported


ERROR 2 [file nvt.mdp]:
  With Verlet lists rcoulomb!=rvdw is not supported


NOTE 2 [file nvt.mdp]:
  Replacing vdwtype=Switch by the equivalent combination of vdwtype=Cut-off
  and vdw_modifier=Potential-switch


ERROR 3 [file nvt.mdp]:
  The box volume is required for calculating rlist from the energy drift
  with verlet-buffer-tolerance > 0. You are using at least one unbounded
  dimension, so no volume can be computed. Either use a finite box, or set
  rlist yourself together with verlet-buffer-tolerance = -1.

Setting the LD random seed to 1821932621
Generated 371091 of the 371091 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 371091 of the 371091 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'GRA'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Setting gen_seed to 925853613
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

There were 2 notes

-------------------------------------------------------
Program gmx grompp, VERSION 5.1.2
Source code file:
/home/usr01/gromacs/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line:
1738

Fatal error:
There were 3 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Here is the NVT.mdp
; Run control
integrator               = sd       ; Langevin dynamics
tinit                    = 0
dt                       = 0.001
nsteps                   = 50000    ; 100 ps
nstcomm                  = 100
; Output control
nstxout                  = 500
nstvout                  = 500
nstfout                  = 0
nstlog                   = 500
nstenergy                = 500
nstxtcout                = 0
xtc-precision            = 1000
; Neighborsearching and short-range nonbonded interactions
nstlist                  = 10
ns_type                  = grid
pbc                      = xy
rlist                    = 1.20
; Electrostatics
coulombtype              = cut-off
rcoulomb                 = 1.20
; van der Waals
vdw-type                 = switch
rvdw-switch              = 0.8
rvdw                     = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                  = no
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; EWALD/PME/PPPM parameters
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
optimize_fft             = no
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps                  = system
tau_t                    = 1.0
ref_t                    = 300
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = -1

periodic_molecules=yes

freezegrps = LIG
freezedim = Y Y Y
; options for bonds
constraints              = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm     = lincs
; Do not constrain the starting configuration
continuation             = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 12

Could you please help to sort out the problem from version 4.6 to 5.1.2
in NVT.mdp
Thanks in advance