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

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 30 20:18:56 CET 2009

Francesco Pietra wrote:
> 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

Again I ask why you are using SPC as the solvent.  If you indeed want to use the 
MARTINI CG water representation, you must pass its configuration explicitly to 
the -cs flag.  Otherwise, the default (spc216.gro) is used.

Are you defining the protein's position in the box before solvation?  Using 
editconf -c is your friend.

> 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.

Well, there are several potential problems.  One is the box size (as I mentioned 
in my last message).  The other question is whether or not the conversion from 
atomistic to CG was done correctly.  I know I have mentioned the problems with 
the MARTINI script a number of times, and perhaps this has also come up in our 
discussions before, but do check that the starting CG coordinates make sense.

Beyond that, try an in vacuo minimization of your protein and see what happens 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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