[gmx-users] Time frames missing

[Mark Abraham]

Hi,

You cannot re-generate the same trajectory, because MD is chaotic and
GROMACS by default is non-deterministic. If your analysis requires
continuity in the trajectory, then you don't ever have any recovery options
other than to go back to some earlier point and run some different
simulation starting from there.

Mark

On Tue, Aug 2, 2016 at 1:07 PM sun.iba2 <sun.iba2 at gmail.com> wrote:

> Dear Sir
>
> Is there a way to start from 159 ns and end it at 166 without checkpoint
> file. Because no checkpoint is there, neither it is backed up. The log file
> is updated till 161ns and when i give state.cpt, the fatal error occurs
> with the follwing msg:
>
> Cannot find log file of 145900 kb.
>
> The information in .trr says that frames till 159 ns are present but the
> .log file is updated till 161.. And that is also incomplete.
>
>
> Is there a ways to continue from 159 ..otherwise i will start from 100 ns
> again.
>
> <div>-------- Original message --------</div><div>From: Justin Lemkul <
> jalemkul at vt.edu> </div><div>Date:02/08/2016  3:12 AM  (GMT+05:30)
> </div><div>To: gmx-users at gromacs.org </div><div>Cc:  </div><div>Subject:
> Re: [gmx-users] Time frames missing </div><div>
> </div>
>
> On 8/1/16 2:41 AM, Sun Iba wrote:
> > Hello everyone
> >
> > I have extended a 100 ns simulation of a protein in water up to 200 ns.
> > However, the system kept shutting down during the course of simulation
> and
> > i had to restart the runs twice. Following are the files I obtained after
> > completion of mdrun (I am writing information of .xtc only, for .trr its
> > same:
> >
> >
> > *md_0_1.xtc = 0 to 100 ns*
> >
> > *new.xtc = 99.990 to 159.990*
> >
> > *v.xtc = 166.050 to 179.050*
> > *traj-comp.xtc = 179.620 to 200.00 ns*
> >
> > Now I am surprised to see that the time frames from 159.990 to 166.050
> are
> > not written to any file. I have also checked the .trr and .xtc file with
> > gmx check and found that time frames are incomplete after the follwoing
> > command:
> >
> >  gmx check -f new.trr
> >
> > Checking file new.trr
> > trn version: GMX_trn_file (single precision)
> > Reading frame       0 time 99990.000
> > # Atoms  133688
> > Reading frame    6000 time 159990.000
> >
> > *WARNING: Incomplete frame: nr 6607 time 166060*
> >
> > Item        #frames Timestep (ps)
> > Step          6607    10
> > Time          6607    10
> > Lambda        6607    10
> > Coords        6607    10
> > Velocities    6607    10
> > Forces           0
> > Box           6607    10
> >
> > Now I am not sure to catenate the avaialble file or should i start the
> run
> > again from 159.990 to 166.050? iF YES, WHAT WOULD BE THE COMMAND FOR
> THAT...
> >
>
> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
>
> -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
>
> ==================================================
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