Please keep requests for help on the list. That way they're archived for others to use, and other people can raise points of interest.
The last sentence here http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off is my suggestion for you :-) Probably, you have only one [molecule] statement for your two molecules, and by chance you included it first so that there was no error message from grompp. If you don't understand why this is a problem, find the relevant section of Chapter 5 of the manual - or read the whole lot of that chapter! :-) Mark ---------------------------- Original Message ---------------------------- Subject: How simulate two peptides in a box? From: [EMAIL PROTECTED] Date: Sun, July 1, 2007 11:09 pm To: [EMAIL PROTECTED] -------------------------------------------------------------------------- Dear Mark: I'm a graduate student at Tianjin University. I want to simulate two peptides in a box using GROMACS software? I followed your suggestion {set up your topologies (suggest one molecule in each of two .itp files) #include them in the .top file, pick a starting configuration for both of them in the same structure file, solvate, minimize.} But when I minimized the system, I got the information ¡±1-4 interaction between 83 and 85 at distance 1.862 which is larger than the 1-4 table size 1.000 nm¡±. I checked the topology and found that atom 83 belong to one peptide and the atom 85 the other peptide. That¡¯s to say the two peptides were considered as a peptide. Can you tell me how to do? I'd be very happy and grateful if you could tell me how to do it. Looking forward to your reply. Best regards. Fufeng Liu _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
