Hi all, Wonderful community here! FAQs andManuals on one side, nothing beats the advice of experts. Whoever started this forum, thank you. I am learning a lot.
I have a question of my own. I am trying to see the interaction of certain surfactants and co-surfactants at a hydrophobic interface. To that end I have made a gro and top file using the element carbon, minimizing its box size to approximately its atomic radius 0.1nm by editconf, concatenating it by genconf 100 times in x and y directions but only once in z, giving 10000 carbon atoms. This generates a very nice surface. Then I follow up with editconf again to increase the size of the configuration file in the z direction to 10nm as well. So the end result is a 10x10x10nm box with a hydrophobic carbon wall on one side of the box. The wall's integrity is maintained using position restraints of a point for each carbon. To check the correctness of this procedure, I performed a minimization, however, during preprocessing using grompp a fatal error occurred: Last line read: '[ molecules ]' Invalid order for directive molecules I would like to inquire as to what this error is and how to avoid it. Just to verify if the manually produced topology or the configuration files were correct, I processed a benzene ring through the same procedure, ending up with the same error. Here is the topology file: #include "ffgmx.itp" [ moleculetype ] ; Name nrexcl carbon 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 C 1 carbon CAN 1 0.000 12.0350 [ position restraints ] 1 1 1000 1000 1000 ; restrain every carbon atom to a point [ molecules ] carbon 10000 Any help would be highly appreciated. Cheers, Ali -- 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/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/mailing_lists/users.php