On 07/02/2013 01:34 PM, Justin Lemkul wrote: > On Tue, Jul 2, 2013 at 7:26 AM, Humphrey Morhenn < > humphrey.morh...@frm2.tum.de> wrote: > >> Dear users, >> >> there seem to be alot of frames missing in my .trr trajectory file and I >> wonder if anyone knows how to recover the (hopefully not lost) information. >> >> tinit = 0 >> dt = 0.001 >> nsteps = 120000000 >> nstxout = 1000000 >> >> When I e.g. run trjconv -pbc mol -f (.trr) -s (.tpr) -o (.trr), it says: >> Reading frame 0 time 77000.000 >> Reading frame 30 time 107000.000 -> frame 30 time 107000.000 >> >> What happened to the frames <77ns and >107ns? >> >> > When running trjconv, trjcat, etc, Gromacs reports the frame it is reading > and then over-writes the line as it progresses through the trajectory. You > have 30 frames spanning 30 ns, which is exactly what your .mdp file > specifies. You haven't posted any information (previous protocol, > remainder of .mdp, etc) that would indicate why the trajectory starts at 77 > ns. > > -Justin >
Ok, I checked the trajectory with gmxcheck, and indeed the file ends at 120ns. But still, there are only 44 frames in the file, instead of 121 as specified in the .mdp file. The .trr file was not modified after the simulation. The simulation itself was performed on a cluster with v4.5.4, using the options -npme -1 -s (.tpr) -deffnm () -cpi -append for ALL consequtive runs. The energy and log files are both complete. It seems like the trajectory file was not appended, but overwritten instead? The input .mdp file for grompp is constraints = none integrator = md dt = 0.001 ; ps ! nsteps = 120000000 nstcomm = 1 nstenergy = 100 nstcalcenergy = 10 nstxout = 1000000 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 2.0 fourierspacing = 0.15 optimize_fft = yes Tcoupl = Nose-Hoover tau_t = 4.0 ref_t = 509 Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 20.0 compressibility = 4.5e-5 ref_p = 1.01325 Regards, Humphrey
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