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

[Justin Lemkul]

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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