[gmx-users] failing of g_membed

[Netaly Khazanov]

Hi All,
I have an aligned structure of protein+ligands in the membrane (a mixture
of DPPC and DOPC).
The structure is solvated with water (gmx solvate -cp
protein_ATP_membrane_box.gro -cs -o protein_ATP_membrane_box_solv.gro -p
topol1.top)
And I used it as input file for g_membed.
grompp_d -c protein_ATP_membrane_box_solv.gro -p topol1.top -f membed.mdp
-o membed.tpr -n
 g_membed_d -f membed.tpr -p topol1.top -o membed_out.trr -x membed_out.xtc
-c membed_out.gro -e -n -xyinit 0.1 -xyend 1.0 -nxy 1000 or
g_membed_d -f membed.tpr -p topol1.top -o membed_out.trr -x membed_out.xtc
-c membed_out.gro -e -n -xyinit 0.1 -xyend 1.0 -nxy 1000 -zinit 1.1 -zend
1.0 -nz 100
it fails with Fatal error:
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 175118.647912, max 39729618.834230 (between atoms 86781 and 86783)
bonds that rotated more than 90 degrees:

Too many LINCS warnings (9639)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
I tried to reduce the time step, it didn't help.
Where should it look in my structure. It is obvious that there are a lot of
overlapping atoms of protein with membrane/water.
Thank you for any help.
Netaly


-- 
Netaly