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 eef
; 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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