[gmx-users] relative constraint deviation after lincs

[Alessandro Casoni]

hi users,
I want to simulate a position restraint md.
pdb2gmx creates a correct protein.top and  a posre.itp file.
but when I use " define = -DPOSRES" I have this error:

Step 1004, time 2.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.026978, max 1.366297 (between atoms 646 and 647)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    646    647   90.0    0.2562   0.2366      0.1000

and the simulation gives me a fatal error...

in my gro file atom 646 and 647 are:
65ASN      N  646   8.608   5.187   2.517
65ASN      H  647   8.510   5.206   2.518

please, give me some tips...

Alessandro