[gmx-users] XTC.error

[He, Yang]

Hi,

I also tried the energy minimization but it seems not to work. In fact, when I run a similar case like this(just including some DNA single strand) ,it is going on well but after I increase some more single DNA strand to the system  it just show such error.

Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel [spoel at xray.bmc.uu.se]
Sent: Sunday, April 26, 2009 12:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] XTC.error

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.
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