[gmx-users] failing of g_membed

[Mark Abraham]

Hi,

As I'm sure you know from reading up on membed, it works by scaling the
embedded protein to be tiny and turning off its interactions. The mostly
likely issue is that you didn't give those instructions correctly. Double
check the documentation, and use a recent version of GROMACS to get the bug
fixes that have happened since your version, which I can see is several
years old.

Mark

On Tue, Jan 8, 2019 at 9:21 AM Netaly Khazanov <netalyk at gmail.com> wrote:

> 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
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