Hi Gromaxers, Thanks for previous answers. I have to simulate reverse micelle after solvation with isooctane.My system now is:
ISOOCTANE(solvent)+AOT(surfactant)+coreWATER. When I do grompp, it says moleculetype SOL is redefined and lots of another errors. Please advice me how do I do reverse micelle simulation. What I did is:: (1) pdb2gmx -f RM.pdb -o RM.gro -p RM.top step :::: I choose isooctane as water model. I have isooctane.itp in the file watermodel.dat inside my forcefield. (2) editconf -c -f RM.gro -o RM1.gro -p RM.top -bt dodecahedron -d 2.0 -shell 0.3 (3) genbox -cp RM.gro -cs isooctane.gro -p reverse_RM.top -o RM2.pdb (4) grompp -f em.mdp -c RM2.pdb -p RM.top -n index.ndx -o em.tpr -maxwarn 5 where RM.pdb is pdb file of reverse micelle All required files I have ,and I have index.ndx file also But it returns : Fatel error: the moleculetype SOL is redefined I tried lots, I change the SOL to WATER every where in frocefield as well as my .gro file too. I tried all what I could but no get any benifit. So Please advice me how do I do this. Thanks for your help. Hari -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
