On 9/12/12 6:57 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
during the mdrun_mpi I get many LINCS warnings like for example:
Step 1143, time 1.143 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.265373, max 1.416702 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
976 979 90.0 0.1072 0.2320 0.0960
But I don't know why. I already minimized my protein. And also in the
grompp run there were no error messages. This was the end of my grompp
output:
processing index file...
Making dummy/rest group for Acceleration containing 80212 elements
Making dummy/rest group for Freeze containing 51274 elements
Making dummy/rest group for VCM containing 80212 elements
Number of degrees of freedom in T-Coupling group System is 102623.00
Making dummy/rest group for User1 containing 80212 elements
Making dummy/rest group for User2 containing 80212 elements
Making dummy/rest group for XTC containing 80212 elements
Making dummy/rest group for Or. Res. Fit containing 80212 elements
Making dummy/rest group for QMMM containing 80212 elements
T-Coupling has 1 element(s): System
Energy Mon. has 2 element(s): Protein non-Protein
Acceleration has 1 element(s): rest
Freeze has 2 element(s): Protein_&_!TYP rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
Estimate for the relative computational load of the PME mesh part: 0.32
writing run input file...
Can you please help me?
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Without a complete description of your system (its contents, previous
minimization and equilibration and their success/failure) and any relevant .mdp
file(s), there's little else that anyone can say.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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