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

Francesco Pietra francesco.pietra at accademialucchese.it
Mon Nov 30 19:49:59 CET 2009

Failed to specify that both the DPPC bilayer and the box of water are
from equilibrated systems in MARTIN web, while the protein was Amber
minimized (and MD) before generating the CG.

I have tried the cg protein alone

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

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

mdrun -v -s topol.tpr

steepest descents converged to machine precision but not to the
requested Fmax < 2000

Pot Ener 7.1e+08
Max force 6.1e+10 on atom 983
Norm of force 2.5e+11

confout.gro shows that one of the subunits has been displaced from the
multimer (apparently both intact) There is a long bond between the
displaced subunit and the rest of the multimer, very closely to the
atom 983 of max force, located in the pore region. I have scarce
experience with gromacs yet, hope that this suggests remedies. I used
a crude version of em.mdp.


---------- Forwarded message ----------
From: Francesco Pietra <francesco.pietra at accademialucchese.it>
Date: Mon, Nov 30, 2009 at 5:36 PM
Subject: Last step before CG em.mdp
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

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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