Dear All,
Hi, I have trajectory file of 500 ns of membrane proteins. Though the file is large enough, I have a problem while I use trjconv option it shows the following error...
Program: gmx check, version 2018.2
Source file: src/gromacs/fileio/xtcio.cpp (line 91)
Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)
Can anybody please help me to solve this error.
Thanks in advance.
With regards
Budheswar
Hi Pritam Kumar Panda
..as the log file is too large I can't upload it but have the summary...appended below...M E G A - F L O P S A C C O U N T I N G
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
W3=SPC/TIP3p W4=TIP4p (single or pairs)
V&F=Potential and force V=Potential only F=Force only
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------------
Pair Search distance check 320006.714048 2880060.426 0.0
NxN Ewald Elec. + LJ [F] 303299731.595520 23657379064.451 97.9
NxN Ewald Elec. + LJ [V&F] 3063936.492928 395247807.588 1.6
1,4 nonbonded interactions 190047.093728 17104238.436 0.1
Shift-X 2379.074646 14274.448 0.0
Bonds 30318.152412 1788770.992 0.0
Propers 219080.270468 50169381.937 0.2
Impropers 4306.486863 895749.268 0.0
Virial 11896.704297 214140.677 0.0
Stop-CM 2379.074646 23790.746 0.0
Calc-Ekin 23788.862604 642299.290 0.0
Lincs 41308.129091 2478487.745 0.0
Lincs-Mat 265989.964104 1063959.856 0.0
Constraint-V 248484.190975 1987873.528 0.0
Constraint-Vir 10358.997924 248615.950 0.0
Settle 55289.310931 17858447.431 0.1
CMAP 1443.577229 2454081.289 0.0
Urey-Bradley 135119.434755 24726856.560 0.1
-----------------------------------------------------------------------------
Total 24177177900.619 100.0
-----------------------------------------------------------------------------
R E A L C Y C L E A N D T I M E A C C O U N T I N G
On 1 MPI rank, each using 6 OpenMP threads
Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
-----------------------------------------------------------------------------
Neighbor search 1 6 10103 356.077 5127.475 4.2
Launch GPU ops. 1 6 2020402 220.061 3168.860 2.6
Force 1 6 1010201 3521.720 50712.442 41.3
Wait PME GPU gather 1 6 1010201 566.769 8161.428 6.6
Reduce GPU PME F 1 6 1010201 100.717 1450.311 1.2
Wait GPU NB local 1 6 1010201 1172.575 16884.975 13.7
NB X/F buffer ops. 1 6 2010299 970.027 13968.295 11.4
Write traj. 1 6 111 3.141 45.224 0.0
Update 1 6 1010201 483.984 6969.319 5.7
Constraints 1 6 1010201 953.615 13731.967 11.2
Rest 186.116 2680.056 2.2
-----------------------------------------------------------------------------
Total 8534.801 122900.352 100.0
-----------------------------------------------------------------------------
Core t (s) Wall t (s) (%)
Time: 51208.808 8534.801 600.0
2h22:14
(ns/day) (hour/ns)
Performance: 20.453 1.173
Finished mdrun on rank 0 Sun Aug 19 19:31:48 2018
How come this could be possible?
I believe that your trajectory is corrupted and i also found similar threads, here it is, maybe you can find more information.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-August/115210.html
https://www.mail-archive.com/[email protected]/msg08934.html
Hi Sanjay Kumar Srikakulam ...What is the solution...? I have generated only the .xtc file no .trr file and it took around more than one month to run in HPC..How can I solve...If i discard the initial 100 ns then its working fine...for me...
Do you have any idea to recover from this problem..
Thanks and Regards
Budheswar
Hi,
I don't know if there is any solution to fix a corrupt file (it's clearly explained in those threads). Since you said the trajectory is fine after removing the first 100 ns, i would suggest you to see up until which frame it is corrupted so you may try to save a bit more than loosing the entire 100ns. If you could have atleast 450 ns, loosing 50 ns will not be a problem as most of the times it maybe considered as a relaxation period.
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