[gmx-users] LINCS error

[deepa rajamani]

Hi,

 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
tried
"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
Deepa Rajamani