Many thanks Justin, It worked!
2009/3/29 Justin A. Lemkul <[email protected]>: > > > Neha Gandhi wrote: >> >> Hi List, >> >> 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated >> annealing followed by production runs of 5ns usng NPT and PBC and >> PME.. After 5ns, the protein moves far away from the ligand. I >> checked the 4ns gro files, the ligand and protein are bound together, >> but its only that 5ns gives issues. >> >> 2) I ran another similar but smaller system and the complex is stable >> even after 8ns. >> >> What went wrong with the simulations in case 1? Is there a way to fix >> this problem? > > Did the protein and/or ligand cross a periodic boundary? If so, trjconv can > "fix" this visualization artifact. > > -Justin > >> Your help is much appreciated. >> >> >> Regards, >> Neha Gandhi, >> School of Biomedical Sciences, >> Curtin University of Technology, >> GPO Box U1987 Perth, >> Western Australia 6845 >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > 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 > -- Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 _______________________________________________ gmx-users mailing list [email protected] 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
