[gmx-users] Restrained MD - lincs error
mynowak at cyf-kr.edu.pl
Thu May 2 14:44:16 CEST 2002
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?
Institute of Pharmacology PAN
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