[gmx-users] Problem in new version of Gromacs 5.0
Mark Abraham
mark.j.abraham at gmail.com
Tue Feb 17 11:53:30 CET 2015
Hi,
"Didn't observe a problem" is different from "working perfectly." In
particular, you are running different simulations now. The phenomenon is
general to all GROMACS and VMD versions.
Mark
On Tue, Feb 17, 2015 at 9:56 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
wrote:
> 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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