Dear Tsjerk Thanks for your suggestion...actually It is a crystal structure...the problem happen when I want to minimize the structure in vacuum....the box size is enough...but the problem is that the minimization is fine with gromacs forcefield but it is not ok with OPLSAA forcefiled....I tried to minimized structure well by gromacs force file and the I took the minimized structure from gromacs forcefield and then I tried it in OPLSAA and the problem was the same as before... I also cut my structure to some pieces ( which I think that it is not reasonable) but I did it but still it is not working....and the interesting point is that the protein is working by gromacs forcefield well without any problem but when I want to use the OPLSAA force field the problem start and I could not minimized my system..I also try the AMBER forcefield but the AMBER also didi not work and the result was the same as OPLSAA, system was exploding.......when I want use all atom the problem appear and I really don't know how to manage it..I already tried different coulomb type algorythm and also different integrator,, different time step..different emtol........but none of them working.......
I would be happy if somebody could suggest me how could I manage it with all atom forcefield... thanks _______________________________________________ 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