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

[Alessandra Villa]

Hi,

mdp option may have been changed going from 4.6 to 5.1 , you should update
your mdp file according  to the 5.1 option
(see http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html
)

If you do not have any special reason to use 5.1, I will suggest to move to
the newest version of GROMACS (GROMACS-2020.1
http://manual.gromacs.org/current/index.html), since you are on the way to
change version.

Best regards
Alessandra



On Sat, Mar 7, 2020 at 11:21 AM Rana Ali <ranadeepu2017 at gmail.com> wrote:

> 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
> --
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