[gmx-users] Re: Constraints - PMF - Different Molecules (Mark Abraham/Arthur Roberts)

Eudes Fileti fileti at ufabc.edu.br
Wed Nov 19 19:25:40 CET 2008

Dear Mark and Arthur, thank you for your reply.
I did what you suggest me and almost everything worked.
I created a topology with the two molecules without bonded parameters
between them and put constrains on two of its atoms.
I did a minimization and a simulation (md integrator).
It worked perfectly. But when I tried to perform the calculation
to free energy using the options below, the simulation
failed. Setting free-energy "no" the simulation works again.
Do you have any suggestions? Bests

; Free energy control stuff
free-energy              = yes
init-lambda              = 1.0
delta-lambda             = 0
sc-alpha                 = 0
sc-power                 = 0
sc-sigma                 = 0.3

Error Message:
Back Off! I just backed up dgdl.xvg to ./#dgdl.xvg.9#
starting mdrun 'C60 - PMF'
30000 steps,     60.0 ps.

Back Off! I just backed up traj.trr to ./#traj.trr.18#
step 0Warning: 1-4 interaction between 5 and 28 at distance 1.398 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

> Arthur Roberts wrote:
> > Dear Eudes,
> >
> > You need to technically make it 1 "big molecule".  As long as there are
> > no bonds specified between molecule A and B.  The big molecule will
> > behave as if there are two molecules in it.  I do it to dock small
> > molecules to proteins.
> That's a good description, Arthur, thanks.
> > 1) Combine molecules A and B into a big structure file (i.e. pdb or gro).
> > 2) Edit this file, so that they are the same chain.
> > 3) run pdb2gmx
> > 4) Change all the residue names to MOL and change Protein_A to MOL in
> > the top and pdb files.
> > 5) Make sure that there is no bonds between molecule A and B in the top
> > file.  There probably won't be, but it is good to check anyway.
> > 5) run grompp to check this file to see if it is acceptable to gromacs.
> > 6) add distance restraints after the improper dihedrals.  If you put it
> > anywhere else, it will not work.
> That contradicts the description of the topology file format on (e.g.)
> page 109 of the GROMACS 4 manual - "starting with GROMACS 3.1.3 all
> directives at the parameter level can be used multiple times and there
> are no restrictions on the order, except that an atom type must be
> defined before it can be used in other definitions."
> > 7) run grompp again to check this file to see if it is acceptable to
> gromacs
> >
> > Other advise:
> > 1) I would roughly dock the molecules together, so that you don't have
> > to have such a large water box.
> > 2) I would experiment with force constants and time constants for the
> > distance restraints.  A useful article is:
> Mark
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