[gmx-users] LINCS error
deepsri at bu.edu
Fri Jan 21 21:40:22 CET 2005
I have been trying to run MD of a chopped section of protein, this
leading to several cut free ends in the protein.
When I try to run position restraint MD on this I get Lincs warnings
saying the following :
Step -2, time -0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 3.283886 (between atoms 153 and 155) rms 0.260382
bonds that rotated more than 30 degrees
I searched the Gromacs website and tried a few suggested things like
taking starting from a few frames earlier on from the em.trr file instead
of the last frame from em step. I could not complete this since when I
"trjconv -f frame98.grp -o frame98.trr"
I got an error saying it could not allocate memory.
Are there any suggestions to avoid this LINCS error?
Thanks in advance
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