Dear Justin Very thanks for your quick reply.
> Depends on how you prepared the system. For initial structure of system, I used coordination from website: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html > Probably there were voids in the solvent or lipid headgroups that caused > distortion in the system. When I see the initial structure of system by VMD, There is no voids in the solvent or lipid headgroups, apparently. > Restraints on the lipid headgroups along z could help. I want use restraints on the dopc and chol molecules (lipid molecules). For this purpose, I did following: 1) I used genrestr tool twice. genrestr gave me 2 files (lipidchol.itp and lipiddopc.itp for cholesterol and dopc molecules, respectively). 2) I added define = -DPOSRES in mdp file. 3) I added Include Position restraint file to the topology file. My topology file is as follows: ; Include forcefield parameters #include "gromos-43a1-s3_lipid.ff/forcefield.itp" #include "cholesterol.itp" ; Include Position restraint file #ifdef POSRES #include "lipidchol.itp" #endif #include "dopc.itp" ; Include Position restraint file #ifdef POSRES #include "lipiddopc.itp" #endif #include "gromos-43a1-s3_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif #include "gromos-43a1-s3_lipid.ff/ions.itp" [ system ] ; Name dopc/chol/sol [ molecules ] ; Compound #mols CHOL 26 DOPC 102 SOL 1706 -------------------------------------------------------------------------------- When I used grompp, I encountered error: Fatal error: [ file lipidchol.itp, line 34 ]: Atom index (30) in position_restraints out of bounds (1-29). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. --------------------------------------------------------------------------------- How to fix this issue? Best wishes -- 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
