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

[Faezeh Pousaneh]

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.
>