[gmx-users] A jump in potential just after extension

[Faezeh Pousaneh]

Dear Justin,

I use gromacs/4.6.7. Below is my .mdp file. No that is not similar to my
case, I do not change any setting for the extension. (I should add that
despite strange jump in potential in g_energy, the trajectory goes in a
direction which I expect.)

************************************PRODUCTIOn************************************************
 integrator                = md
 dt                            = 0.002
 nsteps                    = 50000000
 nstxout                   = 10000           ; save coordinates every  ps
 nstvout                   = 10000           ; save velocities every ps
 nstlog                     = 10000           ; update log file every
 nstenergy               = 10000           ; save energies every
 nstxtcout                = 100000         ; Output frequency for xtc file
 xtc-precision          = 100000         ; precision for xtc file
 ns_type   = grid        ; search neighboring grid cells
 nstlist   = 5            ;  fs
 pbc           = xyz ; 3-D PBC
 rlist           = 1.2 ; short-range neighborlist cutoff (in nm)
 rcoulomb           = 1.2         ; short-range electrostatic cutoff (in nm)
 rvdw             = 1.2 ; 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
 tc-grps                     = LUT SOL         ; two coupling groups - more
accurate
 tau_t                           = 0.1   0.1      ; time constant, in ps
 ref_t                            = 380.   380.     ; reference
temperature, one for each group, in K
 ;tc-grps                       = system
 energygrps                 = LUT SOL
 Pcoupl                        = Parrinello-Rahman
 Pcoupltype                  = Isotropic
 tau_p                           = 1.0
 compressibility             = 4.5e-5
 ref_p                            = 1.0
 gen_vel                        = no
 gen_temp                    = 380.0
 gen_seed                    = 712349
 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
**************************************************************************************************************


Best regards


On Mon, Mar 16, 2015 at 12:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/16/15 4:45 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> I am almost new in Gromacs, I searched about my problem but did not
>> find anything. Can someone please help me?
>>
>> I extend my simulation with same node on same machine, but when I check
>> g_energy I find a sharp jump in potential, why is that so?. (for
>> example if before
>> the extension the average value of potential were X, just as soon as
>> extension starts the average jumps to Y.)
>>
>> my run command:
>>
>> aprun  -n 1   tpbconv_mpi -s production.tpr -extend 100000 -o
>> production.tpr
>> aprun    -n 224  mdrun_mpi -s production.tpr  -cpi state.cpt -c
>> production.gro
>>
>>
> Please post the contents of your original .mdp file.  This issue has come
> up before in very specific cases.  Which version of GROMACS are you using?
>
> Is it related to http://redmine.gromacs.org/issues/1640 ?
>
> -Justin
>
> --
> ==================================================
>
> 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.
>