[gmx-users] Restrained MD - lincs error

[Mateusz Nowak]

Hi gmx_users

I'm trying to run MD in vacuo with position restraints applied to
backbone atoms and some distance restraints as well. The starting
structure is roughly minimized, but it is a homology model with some loops
missing, so it still needs a refinement by MD. The protein consists of 3
seperate chains merged in one [molecule] in topology with -merge command
in pdb2gmx. There were certain proper dihedral types definitions missing,
so I added them manually.

The problem is that I always get lincs error after several steps.

I was trying different force constants in posre.itp file. I also increased
lincs_warnangle, but this didn't help. Then I was trying to apply pos.
rest. to different groups of atoms in the protein (all, main chain, CA),
this also didn't help.

Has anybody any idea what should I do to make it run?

Another question: when I define position restraints in .itp file for,
say, 174 atoms there should be totally 3*174=522 restraints, right?. But
in the screan output from grompp I see the following line:

# POSRES:  348

which equals 2*174. Is this a bug?

Cheers

Mateusz Nowak
Institute of Pharmacology PAN
Krakow
POLAND