[gmx-users] Last step before CG em.mdp

Francesco Pietra francesco.pietra at accademialucchese.it
Mon Nov 30 17:36:15 CET 2009

This is to ask how to proceed to minimize a CG ensemble made of a
transmembrane multimer with pore region immersed in a hydrated DPPC
bilayer and extracellular region immersed in water. Total height 18
nm, width 10 nm in the extracellular region and 6 nm in the pore
region. No clashes/contacts at 1 Angstrom vdw overlap. That is,
cavities had been created - in two steps - with 2.5 Angstrom margin
into both the bilayer surrounding the pore  and the water surrounding
the extracellular region.

Everything worked fine up to creating the topol.tpr, perhaps using a
too small -box 15 15 15. Minimization by steepest descents (em.mdp

cpp                 =  /usr/bin/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  100
;	Energy minimizing stuff
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no


Pot ener 6.6e+15
Max force inf on atom 370

Badly, confout.gro shows the ensemble destroyed, the pieces lying
along a straight line with the water box (that originally surrounded
the extracellular region) at the center.

The commands:

genbox -cp my.pdb -box 15 15 15 -o my.gro

and then the system topology with

grompp -f em.mdp -c my.gro -p my.top -o topol.tpr

and then

mdrun -v -s topol.tpr

I found no way to build the system using gromacs scripts alone, i.e.,
combining preformed gromacs canonical boxes. The way I described above
works fine in Amber with all-atom ensemble.
I would appreciate very much an opinion about the feasibility of such
an approach with gromacs, or, hopefully, if a further solvation step
is needed before minimizing. I did not try with a larger box, or if
the protein+DPPC alone should be solvated with gromacs commands (I
avoided this way because I want to leave the DPPC not solvated from
the sides)...

Thanks for answering

francesco pietra

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