[gmx-users] XTC.error

David van der Spoel spoel at xray.bmc.uu.se
Sun Apr 26 21:13:41 CEST 2009

He, Yang wrote:
> Hi all users,
> When I run the mdrun command, it always shows that XTC.error. Then I check the md.log file and find that:
> There are 220 atoms in your xtc output selection

220 atoms and 3.9e5 bond energy: that is roughly 2000 kJ/mol per bond, 
indicating that bonds on average have been elongated by 1 angstrom. 
Seems your structure is not good...
Try minimizing. And note that gromacs uses nm, in case you have 
generated your own input...

>    Energies (kJ/mol)
>            Bond       G96Angle    Proper Dih.        LJ (SR)   Coulomb (SR)
>     3.91620e+05    9.58742e+03    1.93313e+04   -1.12241e+01    0.00000e+00
>       Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
>     4.20528e+05            nan            nan            nan    0.00000e+00
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.1
> Source code file: stat.c, line: 257
> Fatal error:
> XTC error
> The total energy is shown"nan" I also checked my gro file but there are no lapped atoms. And when I run the command "grompp", there is no any warnings.
> Can anybody tell me what is the problem about this error?
> Thank you very much.
> Yang
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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