[gmx-users] Time frames missing
sun.iba2 at gmail.com
Tue Aug 2 13:06:31 CEST 2016
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>
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
> *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
> 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...
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
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