Dear Gromacs Users,
I am trying to simulate a cell containing different polyatomic species like sulphate, glucose, acetic acid etc. in water. I start my simulation by taking pdb file containing 1 sulphate ion and then add remaining sulphate ions and other species using -cs and -ci from genbox. I use genbox command multiple time till all the species are added and system is solvated in water. But when I perform energy minimisation, the initial system starts with a very high energy i.e. around 10^6 range and the either it doesn't get converged or i get msg Segmentation fault (core dumped). I also tried using genconf but still i was getting the same problem. Can anyone please let me know what is wrong with my system and how can i correctly add all the species in my system. Regards Sukriti [https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
