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

[Faezeh Pousaneh]

yes, but why it was perfectly working with Gromacs 4.6 ? not now. this is
strange for me.


Best regards

On Tue, Feb 17, 2015 at 9:21 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> As Justin's link says, VMD guesses dynamically what your topology is. It
> never saw your .tpr, remember?
>
> Mark
> On Feb 17, 2015 9:00 AM, "Faezeh Pousaneh" <fpoosaneh at gmail.com> wrote:
>
> > Dear Justin,
> >
> > thanks, but I do not find my answer there.
> > My answer must be related to Gromacs new version and VMD version, may
> be, I
> > do not know.
> >
> > Best regards
> > On Tue, Feb 17, 2015 at 12:06 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 2/16/15 5:48 PM, Faezeh Pousaneh wrote:
> > >
> > >> 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?
> > >>
> > >>
> > > http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization
> > >
> > > See #2.
> > >
> > > -Justin
> > >
> > >
> > >  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
> > >> ------------------------------------------------------------
> > >> --------------------------------------------------------
> > >>
> > >>
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
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