[gmx-users] problems with G_membed

[James Starlight]

Dear Gromacs users!

I have some problems with th einsertion of the protein into membrane
via G_membed.


1) first of all I've placed my protein in the desired orientation into
the membrane (overlapping with the lipids)

than I've created input.tpr file via gromp and defined

g_membed -f input.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000
-zinit 1.1 -zend 1.0 -nz 100

mdrun -s input.tpr -membed membed.dat -o traj.trr -c membedded.gro -e
ener.edr  -cpt -1 -mp topol.top


As the result that deleat only overlapping waters but not lipids so
the short g_membed's simulation have been crushed with lincs warnings

Will remove 0 Protein_chain_A molecules
Will remove 0 POP molecules
Will remove 25 SOL molecules

....


Step 8, time 0.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.145418, max 12.037449 (between atoms 6601 and 6602)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   6599   6600   84.9    0.1565   0.2994      0.1435
   6600   6601   88.4    0.1143   0.4880      0.1360
   6601   6602   93.8    0.1078   1.6036      0.1230
   6601   6603  115.3    0.1339   1.0358      0.1530
   6603   6604  103.0    0.1469   0.8389      0.1530
   6604   6605   43.8    0.1697   0.3967      0.1530
   6605   6606   97.9    0.1530   0.6092      0.1530
   6606   6607   58.3    0.1622   0.1140      0.1530
   6609   6610   36.3    0.1546   0.1783      0.1530
   6618   6619   36.1    0.1550   0.1795      0.1430
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 6602 and 6604
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


How I could fix it that g_membed deleate overlapped lipids as well ?


2) Also I wounder to know if it possible to launch g_membed with in
the gpu supported mode ?

when I add to the membed.mdp
cutoff-scheme = Verlet
I've obtained that I cant not use
energygrp_excl = Protein Protein

Thanks for help

James