[gmx-users] failing of g_membed

[Netaly Khazanov]

Thank you for your replay.
I will check it out

On Wed, Jan 9, 2019 at 6:58 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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-- 
Netaly