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: [email protected] [[email protected]] On Behalf
Of David van der Spoel [[email protected]]
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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