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

[Mark Abraham]

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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>