[gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995)
amit.kumawat20 at gmail.com
Thu Dec 25 11:00:04 CET 2014
Thank you very much David. Out of the complete trajectory I identified all
those frames which are corrupted and manually concatenated the rest of the
trajectory. Can you provide me suggestion for the possible source of error.
Because in the log file I could not see any out of disk space error and I
have been using the same version of gromacs for initiating or extending
Amit R. Kumawat
Junior Research Fellow,
C/O Dr. Suman Chakrabarty
Physical & Materials Chemistry Division
CSIR-National Chemical Laboratory
Pune, India - 411008
On Wed, Dec 24, 2014 at 8:56 PM, David van der Spoel <spoel at xray.bmc.uu.se>
> On 2014-12-24 15:33, Amit Kumawat wrote:
>> Dear Gromacs Users,
>> I have a trajectory of 2microsecond.
>> I am trying to use gmxcheck to analyse trajectory but I am getting
>> following error;
>> Program gmxcheck, VERSION 4.6.5
>> Source code file: /home/suman/sources/gromacs-4.6.5/src/gmxlib/xtcio.c,
>> line: 92
>> Fatal error:
>> Magic Number Error in XTC file (read 0, should be 1995)
>> I have seen similar questions in the mailing list describing the
>> may be corrupted. If its true in all the cases of this error, Is there any
>> way to recover the trajectory?
>> Please provide suggestion to solve the error.
> start with
> trjconv -f old.xtc -o new.xtc
> to see how much is corrupt.
>> Amit R. Kumawat
>> Junior Research Fellow,
>> Physical & Materials Chemistry Division
>> CSIR-National Chemical Laboratory
>> Pune, INDIA
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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