HI guys, I got this problem when I running my protein and metal in mix solvent. First of all,my question is can we use the original file of pdb and dock it with metal and run it by simulation?
Second question, after the equilibration part where the pressure and temperature is on.The pressure that I need is should be 1 bar but the result that i had first is in negative value but after extend the time steps the average of the pressure become positive with the value was 1.6 bar. Therefore I continue to MD production by using the equili.gro file. Not so long after that the system said that my protein in this simulation was explode and results shows it produce a lot of pdb file at the certain step.Can you tell me why it is happened? I have no idea with this situation. -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com -- 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/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
