[gmx-users] XTC.error

[Mark Abraham]

He, Yang wrote:
> 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.

"seems not to work" is a description of a problem that can't get you any 
effective help. We're not the family doctor who you're paying to ask you
probing questions. You need to describe fully :-)

In any case, I agree with DvdS that you've got some gross problem with 
your starting structure.

Mark

> 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.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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