[gmx-users] Time frames missing

[Justin Lemkul]

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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