[gmx-users] Problem in new version of Gromacs 5.0

[Faezeh Pousaneh]

Dear expert,

I have upgraded my Gromacs to latest version 5. I try to run my tested
simulations in new version, but strangely I see in VMD file of the
trajectory that some unwanted bonds occur during the simulation (I have
tried for difference molecules, even simple water). I wonder is there
something wrong in my .mdp file which must be adopted to the new version of
Gromacs, or is it some kind of effect of periodic boundaries condition
which appear in the VMD?

my .mdp file (which was working well in Gromacs4.6):


 integrator                = md
 dt                        = 0.002
 nsteps                    = 1000000
 nstenergy                 = 1000        ; save energies every
 nstxtcout                 = 10000       ; Output frequency for xtc file
 xtc-precision             = 10000       ; precision for xtc file
 ns_type                   = grid        ; search neighboring grid cells
 nstlist                   = 5           ;  fs
 pbc                       = xyz         ; 3-D PBC
 rlist                     = 1.0         ; short-range neighborlist cutoff
(in nm)
 rcoulomb                  = 1.0         ; short-range electrostatic cutoff
(in nm)
 rvdw                      = 1.0         ; short-range van der Waals cutoff
(in nm)
 coulombtype               = PME         ; Particle Mesh Ewald for
long-range electrostatics
 pme_order                 = 4           ; cubic interpolation
 fourierspacing            = 0.16        ; grid spacing for FFT
 vdw-type                  = Cut-off
 Tcoupl                    = v-rescale   ; modified Berendsen thermostat
 tau_t                     = 0.1         ; time constant, in ps
 ref_t                     = 298.        ; reference temperature, one for
each group, in K
 tc-grps                   = system
 Pcoupl                    = Parrinello-Rahman
 Pcoupltype                = Isotropic
 tau_p                     = 1.0
 compressibility           = 4.5e-5
 ref_p                     = 1.0
 gen_vel                   = no
 DispCorr                  = EnerPres    ; account for cut-off vdW scheme
 constraints               = all-bonds   ; all bonds constrained (fixed
length)
 continuation              = yes         ; Restarting after NPT
 constraint-algorithm      = lincs       ; holonomic constraints
 lincs_iter                = 1           ; accuracy of LINCS
 lincs_order               = 4           ; also related to accuracy

many thanks in advance,

Best regards
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