I downloaded the benchmark files from the website:
http://amber.scripps.edu/amber8.bench2.html and to test the charmm on my linux cluster.
First, I run it with single processor, everything is fine and it took about 16 min.
Then I setup for dual processors run, but this time I got a lot of warning information :
EPHIFS: WARNING. dihedral 1 is almost linear.
derivatives may be affected for atoms: 1 5 7 8
EPHIFS: WARNING. dihedral 3 is almost linear.
derivatives may be affected for atoms: 1 5 7 10
EPHIFS: WARNING. dihedral 5 is almost linear.
derivatives may be affected for atoms: 1 5 18 20
EPHIFS: WARNING. dihedral 7 is almost linear.
derivatives may be affected for atoms: 2 1 5 7
EPHIFS: WARNING. dihedral 9 is almost linear.
derivatives may be affected for atoms: 3 1 5 6
EPHIFS> Total of 2841 WARNINGs issued.
TOTAL ENERGY CHANGE EXCEEDED
20. KCAL AND 10% OF THE TOTAL KINETIC ENERGY IN THE LAST STEP
PREVIOUS E = nan CURRENT E = nan KINETIC = nan
Writing RESTART FILE with previous and current coordinates,
which may be read by: READ COOR DYNR .... (see io.doc).
NOTE!! THIS FILE C A N N O T BE USED TO RESTART A RUN!!!
***** LEVEL -2 WARNING FROM
*****
***** ENERGY CHANGE TOLERANCE EXCEEDED
then stop.
I do not understand why, I use the same input file and same version of charmm on same machine. Is there anyone help me out this problem? Thanks.
