Hi Jose, I will start by telling you that I do not have an exact answer for your problem since I did not encounter this particular problem myself. However, your are reply-less for 3 days already so better a crazy idea than no idea. Anyhow, if I am totally wrong, my reply would at least generate some discussion among the outraged people:)
The error appears because you are trying to include the file for the restraints on the lipids on the bilayer margin from your system after the martini_v2.0_lipids.itp. You do not have an .itp of your bilayer. So, this is why it is tempting to do what you did. However, your bilayer is formed of a multitude of the POPCs or POPGs defined in martini_v2.0_lipids.itp. On top, you want only a certain fraction of them to be restrained. According to the 'rules' of GROMACS, the restraints have to be included after finishing defining [moleculetype]. Moreover, in the [position_restraints] the ai indices must respect the indices of the atom/particle in the [moleculetype], not the system. (http://www.gromacs.org/Documentation/How-tos/Position_Restraints). Your problem is similar to the case of defining position restraints for water: ; Include water topology #include "oplsaa.ff/spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif I.E. Here you have the topology defined for one molecule of water that you multiply in your system, but the restraints are also defined only for that molecule of water, and by extension to all molecule of water in the system. This is why it is difficult to distinguish between different POPCs/POPGs since the restraints can be defined either for all POPCs/POPGs or for none. Crazy solution: rename the POPCs/POPGs on the margin of the bilayer (the ones you want to restrain) into a new moleculetype i.e. POPCr (*r*estrained) in the .gro file. Modify the martini_v2.0_lipids.itp to include your POPCr by copying all the parameters from POPC. However, after the definition of POPCr inside this file, not in the .top file (as you tried before), include: #ifdef LIPID_RES ; Position restraint for each POPCr [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 2 1 1000 1000 1000 ..... 13 1 1000 1000 1000 #endif Moreover, in the .top file subtract from the POPC the number of restrained POPC and add a new line for POPCr. Do the same for POPG. Hope this helps, Andreea -- View this message in context: http://gromacs.5086.n6.nabble.com/restraints-placed-on-the-boundary-region-of-a-lipid-membrane-tp4999983p5000054.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
